Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA
Figure 9
Native contacts between DPO4 and DNA in native bound structure.
(A) Native contacts for each nucleotide in DNA. DPO4 interacts with DNA in native bound structure at three different regions, which are colored orange, olive green and dark cyan, corresponding to the major groove, minor groove and the terminal of the DNA duplex, respectively. (B) Native contacts for the sugar, base and phosphate group in DNA. (C, D) The native structure of DPO4-DNA binary complex. In (C), the sugar, base and phosphate groups in DNA are colored from blue to red, corresponding to contact number from 0 to 5; while DPO4 is colored grey. In (D), the residues in DPO4 are colored from blue to red, corresponding to the DPO4-DNA contact number from 0 to 5, while DNA is colored grey. The DPO4-DNA contacts are drawn by orange lines in (C) and (D).