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Distances
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RNA H-Head
a
-helix (19 bp length in Å units)
Dimameter of Double
a
-Helix (length in Å units)
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The HammerHead Ribozyme Structure for Molecular Biology
The RNA HammerHead Complex.
The yeast GAL4 Protein is a transcriptional activator that binds to DNA. The DNA is shown using
Sticks
with the bases colored Shapely, and the backbone colored red. The two subunits of the symmetric dimer are shown using the
Backbone
display. The DNA recognition module is blue; the linker region is purple; and the dimerization element is green. The two metal ions bound to each subunit are shown as yellow balls. (
cf.
Fig. 3 of Marmorstein,
et al.
)
Close-up view of protein-DNA interactions in one half-site.
Protein residues H-bond to the DNA bases as follows: Lys17 (carbonyl) to C8; Lys18 (carbonyl) to C7 and C8; and Lys18 (amino) to G6 and/or G7.
The protein also makes these contacts to the DNA sugar-phosphate backbone: Gln9 and Arg15 with phosphate 5; and Lys20, Cys21 (NH), and Lys23 with phosphate 6. (
cf.
Figs. 5 & 6 of Marmorstein,
et al.
)
Show H-bond distances to:
DNA bases;
DNA backbone.
(Zoom-in to see the individual contacts.)
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Coordinates from 1D66.pdb.
