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Figure 5.
Figure 5. Comparison of the D20A mutant bound to different
DNA sites and comparison with wt Zif268 structure. (a) Region of
the D20A-GCG structure focusing on the interacting residues.
Broken lines indicate hydrogen bonds. Simple modeling indicates
that Glu21 could not obtain this new conformation in the
wild-type complex without making electrostatically unfavorable
contacts with Asp20. Modeling also suggests that this new Glu21
conformation would collide with the thymine methyl group if the
mutant was bound to a Image site and this observation fits
nicely with the binding data for the two proteins at the Image
and Image sites. (b) Same region of the wild-type Zif268
structure[16] shown in previous panel. (c) Comparison of the
interaction between Glu21 and Arg18 in the D20A- Image structure
with the interaction between Asp20 and Arg18 in the wild-type
structure. Broken lines indicate hydrogen bonds and distances
are given in Å. (d) Corresponding region of the D20A-GCT
structure. Only the most relevant contact made by the secondary
Arg18 conformation is shown for clarity. We explored the
possibility that the electron density modeled as an ordered
water was actually due to an alternate conformation of Arg18,
but we were not able to fit the Arg18 guanidinium group into
this density without severely distorting the side-chain geometry
and generating several unacceptable steric clashes.
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