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Figure 3.
Figure 3 DBD-C modeled on a ssDNA molecule derived from the
DBD-AB/ssDNA co-crystal structure. The DBD-C was aligned with
DBD-B as shown in Figure 2C and then docked onto the 3 nt DBD-B
binding site (shown in red). Side chains in DBD-C (the position
for Y581 is putative) that are orientated to interact with the
sugar-phosphate backbone are colored in green and blue (for
carbon and nitrogen atoms, respectively), and those in position
to hydrogen bond, or stack with, DNA bases are yellow. Putative
hydrogen bonds with the phosphate groups are shown as dashed
lines. The position of conserved C486 is shown as a reference.
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