@text Protein Science 1994 - Vol. 3, Issue 10 "THE PROTEIN TOURIST #8 - THE T-R, DEOXY-OXY TRANSITION IN HUMAN HEMOGLOBIN" David Richardson, Celia Bonaventura, and Jane Richardson Kin.1- Hb tetramer: deoxy vs oxy transition animated Kin.2- Hb T-R transition: alpha chain and heme closeup Kin.3- The alpha1-beta2 allosteric interface Kin.4- Alpha1-alpha2 salt bridges Kin.5- Beta2 salt bridges Then return to Kin.1, to correlate details with overview For hemoglobin, its function as an oxygen-carrier in the blood is fundamentally linked to the equilibrium between the two main states of its quaternary structure, known as the unliganded "deoxy" or "T state" versus the liganded "oxy" or "R state". We will use animated kinemages to illustrate the structural changes that occur during this transition and how such changes result in important functional properties, such as cooperativity of oxygen binding and allosteric control by pH and anions. Hemoglobin is not a pure two-state system, but the T to R transition provides the major, first-level explanation of its function and is the focus of this ProTour. The hemoglobin molecule (which we will sometimes abbreviate as "Hb") is a tetramer of two alpha and two beta chains; in human they contain 141 and 146 residues respectively. They are different but homologous, and they share an all-helical tertiary structure known as the "globin fold". In all of these kinemages, the deoxy T state is shown in shades of blue and the liganded R state in shades of pink, with the alpha chains slightly paler than the beta chains. The two crystal structures illustrated here are human deoxy hemoglobin, which is in the T-state quaternary structure with no ligands at the O2-binding site, and human carbonmonoxy hemoglobin, which is in the R-state quaternary structure and has ligands at all 4 sites. These two were the first matched pair of Hb structures solved at fairly high resolution, and were the subject of detailed comparisons (Baldwin & Chothia). Protein Data Bank (PDB) files 3HHB and 1HCO do not need to be realigned for most comparisons, although they include only a non-redundant half-dimer; the full tetramer coordinates are available on-line from Brookhaven (130.199.144.1) in directory /user_group/biological_units, as files pdb3hhb.bio and pdb1hco.bio. Kinemage 1 shows multiple views of the quaternary-structure change for a tetramer of human hemoglobin. Click on the "ANIMATE" button to change between the T-state (deoxy) and R-state (oxy) forms. The unliganded T-state is shown in shades of blue (bluetint alpha-chains, cyan betas, and skyblue hemes) and the liganded R-state is in shades of pink (pinktint alphas, pink betas, and hotpink hemes), suggestive of the change in color between deoxygenated and oxygenated blood. The structure is simplified by showing only the Calpha backbones. View1 looks down one of the approximate 2-fold axes, with alpha subunits at the top and beta subunits at the bottom. Notice that the hemes are quite far apart, so that their interactions must be mediated by the protein. The unliganded (deoxy) form is called the "T" (for "tense") state because it contains extra stabilizing interactions between the subunits , which we will see in detail in Kin. 4 and 5. In the high-affinity R-state conformation the interactions which oppose oxygen binding and stabilize the tetramer are somewhat weaker or "relaxed". In some organisms this difference is so pronounced that their Hb molecules dissociate into dimers in the oxygenated form. Liganded human Hb will also dissociate when diluted, which poses problems for cell-free Hb-based blood substitutes because the dissociated protein is rapidly excreted. Try animating in View2 (choose from the "Views" pulldown menu), which looks down the exact crystallographic 2-fold axis from the Beta1-Beta2 end. The yellowtint crosses are phosphate sites present in deoxy but not oxy Hb. In oxy Hb, the beta subunits move closer together, squeezing out phosphates (such as 2,3 DPG), and allowing the N- and C-termini to interact. DPG and other phosphates bind very much more strongly to the deoxy quaternary structure; therefore they necessarily push the equilibrium toward deoxy Hb, and because of that they decrease O2 affinity. Such regulatory phosphate molecules are useful in the blood, because their concentrations can be controlled to shift the Hb O2-binding curve so that it is working across the steepest and most efficient part under conditions in the lungs and tissues.. The interactions between alpha and beta subunits are critical for cooperativity in oxygen binding. To the first approximation, the Hb molecule consists of two "dimers" (Alpha1-Beta1 and Alpha2-Beta2) which rotate relative to each other as rigid bodies in the R-T transition. View3 looks down the approximate axis around which those Alpha1-Beta1 dimers rotate. Animate with all 4 subunits present, and then turn off Alpha2 and Beta2 in each form to see the rotation for just one dimer. The Alpha1-Beta1 unit undergoes relatively little internal rearrangement, but its overall rotation is considerable. The net rotation of the two dimers alters their interactions with one another, most notably at the allosteric effector site between Beta1 and Beta2 (which we saw in View2) and at the important Alpha1-Beta2 interface (see Kin. 3) where mutations have the largest effect on Hb allosteric properties. After looking at all the other kinemages, come back to this one to see some of those details in the context of the overall tetramer movements. Kinemage 2 shows a single alpha chain of hemoglobin, starting with an overview of the subunit. The 6 major and 2 short alpha-helices that make up the structure of a Hb subunit (the "globin fold") are labeled A through H, which is the traditional naming scheme. For example, the proximal histidine (the tightest protein Fe ligand) is often called His F9, since it is residue 9 on helix F (it is residue 87 in the human alpha chain). The helices form an approximately-cylindrical bundle, with the heme and its central Fe atom bound in a hydrophobic pocket between the E and F helices. Turn on the "highlights" button and choose View2, which is a closeup around the heme O2-binding site. Click the "animate" button to cycle between the deoxy and oxy forms. For this kinemage the two alpha1 heme groups were superimposed on each other, to give a local comparison at this site. The heme is quite domed in the blue T-state (deoxy) form, with the 5-coordinate, high-spin Fe (yellow ball) out of the plane. In the pink R-state form a CO molecule is bound at the left, the Fe, now 6-coordinate, low-spin has moved into the heme plane which has flattenened. The proximal His (at right) connects the Fe to helices on the proximal side, making the Fe position sensitive to changes in the globin structure and vice versa. Remember that this kinemage shows a subunit in the all-unliganded versus the all-liganded states of Hb; when oxygen binds to just one subunit, then its internal structure undergoes some but not all of these changes, depending on conditions. View3 is from an angle that shows the binding site more clearly. O2 binds in the same place as CO, with similar effects on the structure; however, for O2 the outer atom is angled rather than straight. The equilibrium between free and bound O2 is very rapid, with on and off rates that are sensitive to protein conformation. Both CO and NO dissociate from the Fe atom very slowly, so that these gases act as respiratory poisons. The alpha and beta chains differ somewhat in their rates and relative affinities for O2 and other ligands, by virtue of heme-pocket differences, but the differences between affinities in the R vs T quaternary states are much larger. Both alpha and beta chains of Hb resemble myoglobin (the single-chain O2-binder in muscle), both in overall tertiary structure and in using an Fe atom centered in a heme group as the site where oxygen is reversibly bound. The heme is surrounded by a hydrophobic pocket, which is necessary in order for it to bind oxygen reversibly without undergoing oxidation or other undesirable reactions. Choose View4 and turn on "Hphobics" temporarily to see some of the hydrophobic sidechains that form the heme pocket. They actually surround the binding site so thoroughly that O2 cannot get in or out without parts of the protein moving out of the way a bit, so that its dynamic properties are essential to have any O2 binding at all; this restrictive process also increases the specificity of ligand binding. The shift between R and T state requires subunit interactions and does not occur in myoglobin, or in isolated alpha or beta chain monomers. These monomers bind O2 quite tightly, which would work well for loading O2 in the lungs but would not allow unloading it for delivery to the tissues. Therefore, the central critical feature of hemoglobin function is how it achieves, uses, and allosterically controls cooperativity between the 4 binding sites in the tetramer to tune O2 binding for satisfying physiological needs. The binding-site linkage to changes in protein conformation are illustrated in View5 (centered near the OH of Tyr 140), which shows ligand-dependent changes in the region from the heme out to the subunit interface. Linkage of the heme Fe through the proximal His results in tertiary-structure changes that can then transmit their effects to other subunits in the tetrameric assemblage. This allows O2 binding in one subunit to indirectly affect the affinitiy of other subunits. Briefly, inside the alpha chains the R/T equilibrium is reflected in changes in Fe spin state and position as it moves in or out of the heme plane; the proximal His changes distance and angle relative to the heme; the F helix shifts; Tyr 140 moves and its H-bond to backbone weakens; and both the C-terminus of the chain and Arg 141 move significantly at the interface. Changes at the subunit interface (coupled with changes at the Fe, as we have seen) alter the equilibrium between the deoxy and oxy quaternary structures, and conversely a change of quaternary structure alters the balance between the two states inside a given subunit. Each O2 that binds increases the likelihood of switching the tetramer into the oxy state, and once it switches, the O2 affinity at all sites increases because the local structure changes have either already occurred or are easier to make. View6 backs off to show the entire alpha1 subunit, but centered for the whole tetramer (deoxy form), as it was seen in View1 of Kinemage 1. Turn on "axes" to see the 2-fold axes of symmetry of the tetramer. Kinemage 3 shows the critical Alpha1-Beta2 interface, where the subunits shift against each other between deoxy T and oxy R states. The startup view is an overview. Although the symmetry is not exact, similar parts of the subunits contact each other: the C helix, and the "FG corner" between helices F and G. Animate repeatedly, to see the relative motion of these two subunits, with a fairly stationary "hinge" near the top and a larger "ratchet" motion near the bottom. View2 emphasizes the ratchet contact between the C helix of Alpha1 and the FG corner of Beta2; His 97 of the Beta2 FG corner makes a large jump against Thr 38 and Thr 41 of the Alpha1 C helix. View3 emphasizes the hinge contact, where the motions are mainly rotations without much shift, between the Alpha1 FG corner and the Beta2 C helix. "Labels" help identify these parts. Since this is a complex motion orchestrated between the fit of two quite different sets of contacts in the two states, this interface is critical to making Hb allostery work, and mutations of residues in this interface have been found to be especially likely to influence cooperativity and allostery. Kinemage 4 shows the salt links between Alpha1 and Alpha2, which stabilize the deoxy form. View1 is an overview down the exact 2-fold axis between the subunits, showing that there are two equivalent sets of interactions, on either side of the twofold. View2 is a closeup to see the making and breaking of these interactions. Note that Tyr 140 -OH stays close to the carbonyl oxygen of Val 93 in the FG corner, and that Lys 127 from Alpha2 has a strong salt-link to the carboxy terminus of Alpha1 in the deoxy form and in the oxy form has a weaker H-bond to a mainchain carbonyl oxygen. Kinemage 5 shows the salt links at the C-terminus of Beta2, which stabilize the deoxy T form and make a large contribution to the pH dependence of oxygen binding, known as the Bohr Effect . View1 is an overview, from a similar view as in Kin. 3, but this time emphasizing the charged interactions near the C-terminus of the beta chain. View2 is a closeup to see the making and breaking of these interactions. Note that Tyr 145 -OH stays close to the carbonyl oxygen of Val 93 in the FG corner, while His b 146 moves a great deal, disrupting the salt link (charged H-bond) to Asp b 94 that is formed in the T state. Since His titrates near physiological pH, this interaction is quite pH sensitive. At low pH, when more protons are present, the His ring N is more likely to be protonated and positive; this strengthens its H-bond with Asp 94, thus favoring the T state and decreasing O2 affinity. There is also a contribution to the Bohr Effect by charged sidechains in the central cavity of the tetramer, where for instance the anion binding that favors the T state is pH dependent. The pH effect, or Bohr Effect, can be considered as allosteric regulation by the binding of protons. It is important biologically, because it promotes oxygen unloading in the tissues where proton concentrations are elevated, for instance by the production of lactic acid in muscle. To see some of these critical subunit interactions in the context of the whole hemoglobin tetramer, click here: *{Kinemage 1, View 5, master= {details} on}*. Animate, to see details of the T-R changes in the contacts at the allosteric interface between alpha1 and beta2. Choose View6 to see the formation and breakage of the His b 146 salt link, as described in Kin. 5. Choose View7 to look down the central cavity of the tetramer, this time from the alpha1-alpha2 end. Coordinates from Brookhaven Data Bank files: 3HHB & 1HCO (human deoxy hemoglobin vs human CO "oxy") References, for further information: To the structures used here: Baldwin (1980) "The crystal structure of human carbonmonoxy haemoglobin at 2.7A resolution", J. Mol. Biol. 136: 103. (file 1HCO) Fermi, Perutz, Shaanan, & Fourme (1984) "The crystal structure of human deoxy haemoglobin at 1.74A resolution", J. Mol. Biol. 175: 159. (file 3HHB) General treatments of Hb allostery: Perutz (1970) "Stereochemistry of cooperative effects in haemoglobin", Nature 228: 726 Baldwin & Chothia (1979) "Haemoglobin. The structural changes related to ligand binding and its allosteric mechanism", J. Mol. Biol. 129: 175. Dickerson & Geis (1983) "Hemoglobin: Structure, Function, and Pathology", Benjamin/Cummings Publ., Menlo Park, CA Perutz (1989) "Mechanisms of cooperativity and allosteric regulation in proteins", Quarterly Rev. of Biophys. 22: 139-236 Ackers, Doyle, Myers, & Daugherty (1992) "Molecular code for cooperativity in hemoglobin", Science 255: 54 Perutz, Fermi, Poyart, Pagnier, & Kister (1993) "A novel allosteric mechanism in haemoglobin: Structure of bovine deoxyhaemoglobin, absence of specific chloride binding sites, and orogin of the chloride-linked Bohr Effect in bovine and human haemoglobin", J. Mol. Biol. 233: 536 Recent Hb structures in other quaternary states or intermediates: Silva, Rogers, & Arnone (1992) "A third quaternary structure of human hemoglobin A at 1.7A resolution", J. Biol. Chem. 267: 17248 Smith, Lattman, & Carter (1991) "The mutation beta99 Asp-Tyr stabilizes Y - A new, composite quaternary state of human hemoglobin", Proteins: Struct., Funct., Genet. 10: 81 Liddington, Derewenda, Dodson, Hubbard, & Dodson (1992) "High resolution crystal structures and comparisons of T state deoxyhaemoglobin and two liganded T-state haemoglobins: T(alpha-oxy)haemoglobin and T(met)Haemoglobin", J. Mol. Biol. 228: 551 Copyright (c) 1994 The Protein Society. This kinemage is published as part of Protein Science Vol. 3, Issue 10. All rights reserved. This and other kinemages published in Protein Science may be reproduced without permission by teachers and students for research and educational purposes providing this notice remains a part of the kinemage file. In case of doubt or for any other use, contact Cambridge University Press. @kinemage 1 @caption Hemoglobin tetramer - deoxy (blue shades) vs oxy (pink shades) animation. View2 looks down the central cavity, which is wider in the deoxy state, forming phosphate sites. View3 shows the quaternary structure change as rigid rotations of Alpha-Beta dimers (turn off alpha2 and beta2 in both forms). 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asp b 94}P 3.08 -13.39 -15.97 {cb asp b 94}3.88 -14.69 -15.78 {cg asp b 94}2.96 -15.78 -15.29 {od1 asp b 94}1.78 -15.86 -15.56 {cg asp b 94}P 2.96 -15.78 -15.29 {od2 asp b 94}3.48 -16.63 -14.62 {ca his b 146}P 6.51 -16.26 -5.78 {cb his b 146}5.71 -16.99 -4.7 {cg his b 146}4.5 -16.24 -4.2 {nd1 his b 146}4.17 -14.98 -4.66 {ce1 his b 146}3.08 -14.57 -4.03 {ne2 his b 146}2.7 -15.52 -3.2 {cg his b 146}P 4.5 -16.24 -4.2 {cd2 his b 146}3.57 -16.56 -3.26 {ne2 his b 146}2.7 -15.52 -3.2 @kinemage 2 @caption Human hemoglobin alpha1 subunit, deoxy (blue shades) vs oxy (pink shades) structures. Click on "animate" to switch between the two structures, and turn on "highlights" for any of the closeups. View1 shows the overall alpha subunit, Views 2 and 3 are closeups of the heme site, View4 shows the hydrophobic heme pocket, View5 moves out from the heme toward the interface with alpha 2 (alpha 2 not shown), and View6 goes to our standard orientation centered as if in the tetramer: see View1 of Kin.1. @viewid {subunit} @zoom 0.91 @zslab 150 @center 12.158 7.117 -5.574 @matrix 0.62989 -0.30394 0.71474 -0.77650 -0.26621 0.57111 0.01671 -0.91474 -0.40369 @2viewid {heme closeup} @2zoom 2.25 @2zslab 100 @2center 6.566 8.526 -13.842 @2matrix -.99221 .02354 -.1223 .0206 .99947 .02526 .12282 .02254 -.99217 @3viewid {site closeup} @3zoom 2.74 @3zslab 150 @3center 9.087 8.651 -13.833 @3matrix -.94972 .08968 -.29997 .29712 .56024 -.7732 .09870 -.82346 -.55872 @4viewid {pocket} @4zoom 2.11 @4zslab 150 @4center 8.128 7.371 -15.022 @4matrix -.88319 .45277 -.1223 .45328 .89101 .02526 .1204 -.03313 -.99217 @5viewid {interface} @5zoom 2.0 @5zslab 210 @5center -1.215 6.912 -11.206 @5matrix -.991711 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{ca pro a 44}6.334 -4.397 -22.635 {ca his a 45}7.962 -2.357 -25.415 {ca phe a 46}11.432 -2.435 -23.847 {ca asp a 47}14.29 -4.839 -24.019 {ca leu a 48}14.678 -5.353 -20.284 {ca ser a 49}17.773 -7.517 -20.525 {ca his a 50}20.777 -6.497 -18.516 {ca gly a 51}22.63 -3.57 -19.979 {ca ser a 52}19.977 -2.649 -22.471 {ca ala a 53}20.311 0.826 -23.967 {ca gln a 54}16.593 1.4 -23.402 {ca val a 55}16.91 0.869 -19.673 {ca lys a 56}20.094 2.915 -19.437 {ca gly a 57}18.423 5.705 -21.382 {ca his a 58}15.363 5.641 -19.208 {ca gly a 59}17.493 5.51 -16.061 {ca lys a 60}19.172 8.703 -17.119 {ca lys a 61}15.838 10.427 -17.638 {ca val a 62}14.611 9.36 -14.22 {ca ala a 63}17.821 10.532 -12.625 {ca asp a 64}17.728 13.918 -14.356 {ca ala a 65}14.184 14.472 -13.123 {ca leu a 66}15.3 13.708 -9.573 {ca thr a 67}18.227 16.077 -10.02 {ca asn a 68}15.703 18.709 -11.11 {ca ala a 69}13.613 17.966 -8.031 {ca val a 70}16.577 18.335 -5.662 {ca ala a 71}17.455 21.68 -7.26 {ca his a 72}13.887 22.876 -6.723 {ca val a 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asp b 99} 0.73 -4.07 -7.21 @kinemage 4 @caption The Alpha1 - Alpha 2 salt bridges stabilize the deoxy form. View1 is an overview down the 2-fold. 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{ca ser a 52}19.977 -2.649 -22.471 {ca ala a 53}20.311 0.826 -23.967 {ca gln a 54}16.593 1.4 -23.402 {ca val a 55}16.91 0.869 -19.673 {ca lys a 56}20.094 2.915 -19.437 {ca gly a 57}18.423 5.705 -21.382 {ca his a 58}15.363 5.641 -19.208 {ca gly a 59}17.493 5.51 -16.061 {ca lys a 60}19.172 8.703 -17.119 {ca lys a 61}15.838 10.427 -17.638 {ca val a 62}14.611 9.36 -14.22 {ca ala a 63}17.821 10.532 -12.625 {ca asp a 64}17.728 13.918 -14.356 {ca ala a 65}14.184 14.472 -13.123 {ca leu a 66}15.3 13.708 -9.573 {ca thr a 67}18.227 16.077 -10.02 {ca asn a 68}15.703 18.709 -11.11 {ca ala a 69}13.613 17.966 -8.031 {ca val a 70}16.577 18.335 -5.662 {ca ala a 71}17.455 21.68 -7.26 {ca his a 72}13.887 22.876 -6.723 {ca val a 73}13.047 21.103 -3.544 {ca asp a 74}11.131 24.179 -2.275 {ca asp a 75}8.993 24.209 -5.411 {ca met a 76}8.636 20.6 -6.568 {ca pro a 77}4.938 20.764 -7.783 {ca asn a 78}5.955 23.366 -10.347 {ca ala a 79}9.243 21.84 -11.303 {ca leu a 80}7.705 18.422 -11.994 {ca ser a 81}4.416 19.724 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color= blue radius= .2 {nz lys a 127} 10.518 14.958 7.602 {ne arg a 141} -8.517 9.076 -6.403 {nh1 arg a 141} -10.15 7.487 -6.019 {nh2 arg a 141} -8.725 8.129 -4.343 @balllist {sco} color= red radius= .2 {od1 asp a 126} 11.601 5.574 1.869 {od2 asp a 126} 10.796 6.085 3.817 {oh tyr a 140} 0.862 7.482 -12.331 @vectorlist {sc} color= green {ca val a 1}P 7.06 17.792 4.76 {cb val a 1}6.342 18.738 5.727 {cg1 val a 1}7.114 20.033 5.993 {cb val a 1}P 6.342 18.738 5.727 {cg2 val a 1}4.924 19.032 5.232 {ca asp a 126}P 12.985 8.125 1.989 {cb asp a 126}12.821 7.156 3.167 {cg asp a 126}11.649 6.202 2.932 {od1 asp a 126}11.601 5.574 1.869 {cg asp a 126}P 11.649 6.202 2.932 {od2 asp a 126}10.796 6.085 3.817 {ca lys a 127}P 10.972 11.202 2.834 {cb lys a 127}11.393 12.164 3.933 {cg lys a 127}10.409 12.119 5.094 {cd lys a 127}10.908 12.952 6.265 {ce lys a 127}10.113 14.245 6.384 {nz lys a 127}10.518 14.958 7.602 {ca tyr a 140}P -4.347 11.247 -11.236 {cb tyr a 140}-3.868 10.048 -10.417 {cg tyr a 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a 1}-5.66 17.22 -7.28 {c val a 1}-7.15 17.02 -6.98 {o val a 1}-7.84 16.25 -7.66 {ca val a 93}P -1.53 4.53 13.8 {c val a 93}-0.76 4.18 12.52 {o val a 93}-0.22 5.07 11.85 {c val a 93}P -0.76 4.18 12.52 {n asp a 94}-0.73 2.9 12.21 {ca asp a 94}-0.02 2.45 11. {ca tyr a 140}P 4.81 10.98 9.19 {c tyr a 140}5.8 11.36 8.09 {o tyr a 140}6.97 11.67 8.36 {c tyr a 140}P 5.8 11.36 8.09 {n arg a 141}5.31 11.33 6.86 {ca arg a 141}6.16 11.66 5.71 {c arg a 141}6.96 12.84 6.25 {o arg a 141}7.17 12.97 7.47 {c arg a 141}P 6.96 12.84 6.25 {oxt arg a 141}7.4 13.7 5.34 @vectorlist {ca} color= pinktint {c val a 1}P -7.15 17.02 -6.98 {ca leu a 2}-9. 17.66 -5.6 {ca ser a 3}-10.76 19.58 -8.34 {ca pro a 4}-13.47 22.26 -8.79 {ca ala a 5}-15.93 19.46 -9.24 {ca asp a 6}-14.86 16.73 -6.81 {ca lys a 7}-15.21 19.5 -4.19 {ca thr a 8}-18.82 19.64 -5.35 {ca asn a 9}-19.72 15.97 -5.27 {ca val a 10}-18.57 15.87 -1.65 {ca lys a 11}-20.07 19.18 -0.54 {ca ala a 12}-23.2 17.46 -1.89 {ca ala a 13}-23.02 13.82 -0.97 {ca trp a 14}-22.32 14.88 2.59 {ca gly a 15}-25.13 17.57 2.02 {ca lys a 16}-27.67 14.77 2.09 {ca val a 17}-26.07 12.48 4.66 {ca gly a 18}-26.58 15.17 7.27 {ca ala a 19}-28.68 14.55 10.5 {ca his a 20}-27.03 11.14 10.18 {ca ala a 21}-23.27 11.69 9.96 {ca gly a 22}-23.04 10.3 13.49 {ca glu a 23}-24.88 7.01 13.11 {ca tyr a 24}-22.75 6.61 9.98 {ca gly a 25}-19.29 7.31 11.38 {ca ala a 26}-20.05 4.65 13.99 {ca glu a 27}-21.5 2.09 11.59 {ca ala a 28}-18.11 2.38 9.91 {ca leu a 29}-15.95 1.81 12.99 {ca glu a 30}-18.1 -1.26 13.62 {ca arg a 31}-17.34 -2.45 10.09 {ca met a 32}-13.59 -1.85 10.29 {ca phe a 33}-13.45 -3.48 13.73 {ca leu a 34}-15.3 -6.53 12.41 {ca ser a 35}-13.63 -7.03 9.03 {ca phe a 36}-10.03 -6.03 9.64 {ca pro a 37}-9.67 -7.29 13.24 {ca thr a 38}-6.13 -5.93 13.3 {ca thr a 39}-7.27 -2.4 14.1 {ca lys a 40}-8.82 -3.44 17.41 {ca thr a 41}-5.3 -3.16 18.79 {ca tyr a 42}-5.92 0.63 19.4 {ca phe a 43}-9.36 0.69 21.12 {ca pro a 44}-8.48 -1.72 23.96 {ca his a 45}-10.61 0.56 26.07 {ca phe a 46}-13.71 0.14 23.83 {ca asp a 47}-16.61 -2.72 24. {ca leu a 48}-15.81 -2.92 20.27 {ca ser a 49}-19.17 -4.46 20.94 {ca his a 50}-22.24 -3.74 18.8 {ca gly a 51}-24.49 -1.38 20.77 {ca ser a 52}-21.35 -0.17 22.54 {ca ala a 53}-21.87 3.47 23.52 {ca gln a 54}-18.18 4.24 23.1 {ca val a 55}-18.12 3.31 19.42 {ca lys a 56}-21.46 5.11 19.03 {ca gly a 57}-19.88 8.05 20.83 {ca his a 58}-16.82 8.04 18.58 {ca gly a 59}-18.79 7.86 15.32 {ca lys a 60}-19.9 11.3 16.35 {ca lys a 61}-16.24 12.32 16.55 {ca val a 62}-14.96 10.79 13.33 {ca ala a 63}-18.03 12.27 11.71 {ca asp a 64}-17.43 15.69 13.21 {ca ala a 65}-13.93 15.81 11.82 {ca leu a 66}-14.96 14.52 8.4 {ca thr a 67}-17.26 17.49 8.16 {ca asn a 68}-14.77 20.18 9.15 {ca ala a 69}-12.73 18.7 6.34 {ca val a 70}-15.65 18.85 3.9 {ca ala a 71}-15.91 22.45 5.08 {ca his a 72}-12.36 23.8 4.89 {ca val a 73}-11.52 21.35 2.09 {ca asp a 74}-9.51 23.92 0.11 {ca asp a 75}-7.15 23.7 3.06 {ca met a 76}-7.23 20.5 5.08 {ca pro a 77}-3.68 21.04 6.32 {ca asn a 78}-4.77 23.73 8.77 {ca ala a 79}-8.05 22.53 10.04 {ca leu a 80}-7.16 18.94 10.69 {ca ser a 81}-3.84 19.64 12.38 {ca ala a 82}-4.33 18.34 15.99 {ca leu a 83}-5.89 15.13 14.68 {ca ser a 84}-2.74 14.95 12.58 {ca asp a 85}-0.33 15.02 15.52 {ca leu a 86}-2.56 12.97 17.81 {ca his a 87}-2.98 10.24 15.2 {ca ala a 88}0.67 10.5 14.19 {ca his a 89}2.57 11.76 17.22 {ca lys a 90}0.61 10.57 20.26 {ca leu a 91}-0.9 7.33 18.95 {ca arg a 92}1.13 6.05 16.02 {ca val a 93}-1.53 4.53 13.8 {ca asp a 94}P -0.02 2.45 11. {ca pro a 95}-1.09 4.48 7.98 {ca val a 96}-2.44 1.46 6.12 {ca asn a 97}-5.26 1.8 8.64 {ca phe a 98}-6.59 4.99 7.05 {ca lys a 99}-6.96 3.15 3.76 {ca leu a 100}-9.34 0.76 5.5 {ca leu a 101}-11.62 3.06 7.49 {ca ser a 102}-11.56 5.06 4.28 {ca his a 103}-13.12 1.99 2.69 {ca cys a 104}-15.68 1.04 5.32 {ca leu a 105}-16.76 4.68 5.28 {ca leu a 106}-17.59 4.27 1.59 {ca val a 107}-19.26 0.89 2.06 {ca thr a 108}-21.42 3. 4.32 {ca leu a 109}-22.26 6.04 2.18 {ca ala a 110}-23.02 3.26 -0.3 {ca ala a 111}-25.4 1.28 1.91 {ca his a 112}-27.42 4.22 3.22 {ca leu a 113}-27.22 6.26 0.03 {ca pro a 114}-27.96 4.71 -3.36 {ca ala a 115}-29.08 7.33 -5.88 {ca glu a 116}-26.57 10. -4.94 {ca phe a 117}-23.85 7.34 -4.86 {ca thr a 118}-23.2 7.38 -8.61 {ca pro a 119}-19.85 6.23 -9.96 {ca ala a 120}-18.46 9.74 -10.42 {ca val a 121}-19.33 10.44 -6.8 {ca his a 122}-17.88 7.13 -5.65 {ca ala a 123}-14.66 8.53 -7.08 {ca ser a 124}-14.82 11.96 -5.45 {ca leu a 125}-15.63 10.59 -1.99 {ca asp a 126}-12.63 8.32 -2.49 {ca lys a 127}-10.49 11.23 -3.66 {ca phe a 128}-11.74 13.21 -0.68 {ca leu a 129}-10.73 10.61 1.9 {ca ala a 130}-7.43 9.77 0.26 {ca ser a 131}-6.73 13.41 1.12 {ca val a 132}-7.91 13.27 4.72 {ca ser a 133}-5.51 10.38 5.3 {ca thr a 134}-2.61 12.08 3.54 {ca val a 135}-3.16 15.07 5.93 {ca leu a 136}-3.62 12.57 8.81 {ca thr a 137}-0.35 10.89 8.02 {ca ser a 138}1.99 13.86 7.41 {ca lys a 139}4.14 14.47 10.48 {ca tyr a 140}4.81 10.98 9.19 @balllist {scn} color= blue radius= .2 {nz lys a 127} -9.67 12.17 -9.63 {ne arg a 141} 1.79 11.53 3.48 {nh1 arg a 141} 3. 9.77 2.51 {nh2 arg a 141} 0.72 9.92 2.23 @balllist {sco} color= red radius= .2 {od1 asp a 126} -10.19 6.61 -3.79 {od2 asp a 126} -11.47 5.4 -2.67 {oh tyr a 140} 1.47 7.11 13.18 @vectorlist {sc} color= yellow {ca val a 1}P -5.66 17.22 -7.28 {cb val a 1}-5.05 17.6 -6.35 {cg1 val a 1}-4.32 18.8 -7. {cb val a 1}P -5.05 17.6 -6.35 {cg2 val a 1}-5.93 18.02 -5.2 {ca asp a 126}P -12.63 8.32 -2.49 {cb asp a 126}-12.52 7.23 -3.57 {cg asp a 126}-11.3 6.36 -3.36 {od1 asp a 126}-10.19 6.61 -3.79 {cg asp a 126}P -11.3 6.36 -3.36 {od2 asp a 126}-11.47 5.4 -2.67 {ca lys a 127}P -10.49 11.23 -3.66 {cb lys a 127}-10.7 12.05 -4.93 {cg lys a 127}-10.37 11.31 -6.21 {cd lys a 127}-10.8 12.12 -7.43 {ce lys a 127}-10.53 11.37 -8.73 {nz lys a 127}-9.67 12.17 -9.63 {ca tyr a 140}P 4.81 10.98 9.19 {cb tyr a 140}3.72 9.97 8.79 {cg tyr a 140}3.15 9.17 9.97 {cd1 tyr a 140}1.81 8.74 9.89 {ce1 tyr a 140}1.25 7.99 11.01 {cz tyr a 140}2. 7.8 12.11 {oh tyr a 140}1.47 7.11 13.18 {cg tyr a 140}P 3.15 9.17 9.97 {cd2 tyr a 140}3.88 8.95 11.11 {ce2 tyr a 140}3.34 8.22 12.21 {cz tyr a 140}2. 7.8 12.11 {ca arg a 141}P 6.16 11.66 5.71 {cb arg a 141}5.31 12.01 4.47 {cg arg a 141}4.09 11.09 4.25 {cd arg a 141}2.81 11.87 4.49 {ne arg a 141}1.79 11.53 3.48 {cz arg a 141}1.84 10.4 2.73 {nh1 arg a 141}3. 9.77 2.51 {cz arg a 141}P 1.84 10.4 2.73 {nh2 arg a 141}0.72 9.92 2.23 @labellist {lb} color= gold master= {labels} { V}-5.05 17.6 -6.35 { D}-12.52 7.23 -3.57 { K}-10.7 12.05 -4.93 { Y}3.72 9.97 8.79 { R}5.31 12.01 4.47 {heme} -10.43 13.91 18.35 @subgroup {h-bonds} dominant master= {h-bonds} @vectorlist {Hbonds} color= brown {nz lys a 127}P U 9.045 12.054 9.336 {o tyr a 140}U 7.595 11.786 8.654 @vectorlist {Hbonds} color= purple {o val a 93}P U 0.179 5.552 12.164 {oh tyr a 140}U 1.071 6.628 12.866 @kinemage 5 @caption Beta salt bridges, illustrated on beta2. The charged groups at the C-terminus of Beta2 stabilize the deoxy form, with interactions both with other residues on Beta2 itself and Alpha1. View1 is an overview. View2 is a closeup to see the making and breaking of the interactions. Note that Tyr 145 -OH stays close to the carbonyl oxygen of Val 93 in the FG corner. @2viewid {closeup} @2zoom 3.0 @2zslab 290 @2center 4.940 -9.152 -8.207 @2matrix 0.97784 -0.13227 0.16227 0.19013 0.88559 -0.42377 -0.08765 0.44523 0.89112 @group {deoxy} animate dominant @subgroup dominant {alpha1} master= {alpha1} @vectorlist dominant {dummy} master= {beta2} @vectorlist {ca-ca} color= bluetint {ca val a1 1}P 7.06 17.792 4.76 {ca leu a1 2}10.785 18.159 4.237 {ca ser a1 3}12.492 19.934 7.127 {ca pro a1 4}15.511 22.192 6.331 {ca ala a1 5}17.676 19.403 7.724 {ca asp a1 6}16.059 16.945 5.311 {ca lys a1 7}16.809 19.277 2.425 {ca thr a1 8}20.41 19.643 3.508 {ca asn a1 9}20.715 15.845 3.737 {ca val a1 10}19.208 15.283 0.296 {ca lys a1 11}21.393 17.926 -1.357 {ca ala a1 12}24.474 16.497 0.269 {ca ala a1 13}23.747 12.921 -0.738 {ca trp a1 14}22.645 13.719 -4.242 {ca gly a1 15}25.65 15.995 -4.59 {ca lys a1 16}27.926 12.981 -4. {ca val a1 17}25.899 11.07 -6.587 {ca gly a1 18}26.822 13.8 -9.05 {ca ala a1 19}27.749 12.396 -12.429 {ca his a1 20}26.775 8.793 -11.715 {ca ala a1 21}23.135 9.749 -11.417 {ca gly a1 22}22.226 8.131 -14.747 {ca glu a1 23}24.091 4.921 -13.981 {ca tyr a1 24}22.375 4.686 -10.602 {ca gly a1 25}19.009 5.348 -12.224 {ca ala a1 26}19.466 2.37 -14.535 {ca glu a1 27}20.608 0.151 -11.695 {ca ala a1 28}17.549 1.057 -9.635 {ca leu a1 29}15.308 0.145 -12.566 {ca glu a1 30}17.005 -3.199 -13.017 {ca arg a1 31}16.68 -3.889 -9.304 {ca met a1 32}12.978 -3.07 -9.533 {ca phe a1 33}12.322 -5.344 -12.527 {ca leu a1 34}14.025 -8.281 -10.823 {ca ser a1 35}12.66 -7.82 -7.301 {ca phe a1 36}9.137 -6.759 -8.291 {ca pro a1 37}8.342 -8.369 -11.658 {ca thr a1 38}4.849 -6.856 -11.722 {ca thr a1 39}6.476 -3.521 -12.607 {ca lys a1 40}7.553 -4.934 -15.967 {ca thr a1 41}3.927 -4.747 -17.127 {ca tyr a1 42}4.518 -1.055 -17.836 {ca phe a1 43}7.479 -1.702 -20.098 {ca pro a1 44}6.334 -4.397 -22.635 {ca his a1 45}7.962 -2.357 -25.415 {ca phe a1 46}11.432 -2.435 -23.847 {ca asp a1 47}14.29 -4.839 -24.019 {ca leu a1 48}14.678 -5.353 -20.284 {ca ser a1 49}17.773 -7.517 -20.525 {ca his a1 50}20.777 -6.497 -18.516 {ca gly a1 51}22.63 -3.57 -19.979 {ca ser a1 52}19.977 -2.649 -22.471 {ca ala a1 53}20.311 0.826 -23.967 {ca gln a1 54}16.593 1.4 -23.402 {ca val a1 55}16.91 0.869 -19.673 {ca lys a1 56}20.094 2.915 -19.437 {ca gly a1 57}18.423 5.705 -21.382 {ca his a1 58}15.363 5.641 -19.208 {ca gly a1 59}17.493 5.51 -16.061 {ca lys a1 60}19.172 8.703 -17.119 {ca lys a1 61}15.838 10.427 -17.638 {ca val a1 62}14.611 9.36 -14.22 {ca ala a1 63}17.821 10.532 -12.625 {ca asp a1 64}17.728 13.918 -14.356 {ca ala a1 65}14.184 14.472 -13.123 {ca leu a1 66}15.3 13.708 -9.573 {ca thr a1 67}18.227 16.077 -10.02 {ca asn a1 68}15.703 18.709 -11.11 {ca ala a1 69}13.613 17.966 -8.031 {ca val a1 70}16.577 18.335 -5.662 {ca ala a1 71}17.455 21.68 -7.26 {ca his a1 72}13.887 22.876 -6.723 {ca val a1 73}13.047 21.103 -3.544 {ca asp a1 74}11.131 24.179 -2.275 {ca asp a1 75}8.993 24.209 -5.411 {ca met a1 76}8.636 20.6 -6.568 {ca pro a1 77}4.938 20.764 -7.783 {ca asn a1 78}5.955 23.366 -10.347 {ca ala a1 79}9.243 21.84 -11.303 {ca leu a1 80}7.705 18.422 -11.994 {ca ser a1 81}4.416 19.724 -13.447 {ca ala a1 82}4.959 18.276 -16.925 {ca leu a1 83}5.964 14.919 -15.461 {ca ser a1 84}2.869 14.72 -13.246 {ca asp a1 85}0.713 15.445 -16.288 {ca leu a1 86}2.515 12.731 -18.208 {ca his a1 87}2.094 10.06 -15.577 {ca ala a1 88}-1.478 11.037 -14.766 {ca his a1 89}-2.929 11.277 -18.255 {ca lys a1 90}-0.735 9.142 -20.422 {ca leu a1 91}1.384 6.528 -18.674 {ca arg a1 92}-1.119 5.987 -15.826 {ca val a1 93}1.148 3.881 -13.67 {ca asp a1 94}-0.654 2.617 -10.574 {ca pro a1 95}0.556 4.665 -7.552 {ca val a1 96}1.726 1.549 -5.661 {ca asn a1 97}4.639 1.154 -8.075 {ca phe a1 98}6.198 4.46 -7.011 {ca lys a1 99}6.97 2.914 -3.654 {ca leu a1 100}8.699 0.027 -5.281 {ca leu a1 101}10.965 2.199 -7.388 {ca ser a1 102}11.65 4.449 -4.389 {ca his a1 103}12.814 1.47 -2.37 {ca cys a1 104}15.097 0.286 -5.174 {ca leu a1 105}16.567 3.758 -5.55 {ca leu a1 106}17.285 3.775 -1.814 {ca val a1 107}18.979 0.366 -2.091 {ca thr a1 108}21.061 1.595 -5.018 {ca leu a1 109}22.19 4.656 -3.075 {ca ala a1 110}23.011 2.496 -0.044 {ca ala a1 111}25.155 0.207 -2.171 {ca his a1 112}27.15 3.085 -3.625 {ca leu a1 113}27.409 5.616 -0.83 {ca pro a1 114}28.861 3.639 2.11 {ca ala a1 115}29.932 6.735 4.025 {ca glu a1 116}26.954 9.054 3.194 {ca phe a1 117}24.068 6.712 3.876 {ca thr a1 118}23.71 7.392 7.595 {ca pro a1 119}20.419 6.648 9.455 {ca ala a1 120}19.477 10.327 9.297 {ca val a1 121}20.262 10.609 5.592 {ca his a1 122}18.365 7.388 4.908 {ca ala a1 123}15.346 8.891 6.637 {ca ser a1 124}15.621 12.141 4.687 {ca leu a1 125}16.003 10.345 1.363 {ca asp a1 126}12.985 8.125 1.989 {ca lys a1 127}10.972 11.202 2.834 {ca phe a1 128}12.173 12.96 -0.255 {ca leu a1 129}11.281 10.065 -2.562 {ca ala a1 130}7.844 9.886 -0.977 {ca ser a1 131}7.347 13.584 -1.7 {ca val a1 132}8.414 13.161 -5.311 {ca ser a1 133}6.011 10.219 -5.591 {ca thr a1 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