Fig. 8

Comparison of Form A and Form B. The atomic model of PolD was aligned by superimposing the DP2 (except the modeled CTD) region of Form A (purple) and Form B (pink). a Top view. b Side view. c Bottom view. d Side view of both forms. (DP1 (Form A), cyan; DP1 (Form B), khaki; DP2 (Form A), purple; DP2 (Form B), pink; DNA (Form A), blue; DNA (Form B), red. The DNA duplex rotates 40° in the conversion from Form A to Form B. e Enlarged view of the DNA-PolD interacting region (bottom view). The modeled DP2-CTD (orange broken line) region rotates about 11° in conjunction with DP1. The catalytic domain of DP2 (DP2-Cat) is indicated by the green broken line. f Enlarged view of the DNA-PolD interacting region (side view). The active site residues D965 and D967 are colored gold (Form A) and red (Form B). The positions of the side chains of active site residues are those of crystal structures and should be regarded as approximate ones. Note that the PCNA region of the model is omitted for clarity (a–f)