FIGURE 6.

Active site conformations and base pairing configurations in hpol η-DNA-dNMPNPP insertion-step complexes. Views are into the active sites from the major groove side (panels on the left) and rotated by 90° around the horizontal axis and looking roughly along the normal to the nucleobase plane of the incoming dNMPNPP (panels on the right) for four hpol η complexes. The polymerase is shown as a schematic, and the DNA template-primer duplex and selected hpol η side chains are shown in stick form (e.g. finger residues Gln-38 and Arg-61; carbon atoms colored in beige). Oxygen, nitrogen, and DNA phosphorus atoms are colored in red, blue, and orange, respectively, and Mg²⁺ ions are drawn as light green spheres. Hydrogen bonds are dashed lines. A, complex with template G paired to incoming dCMPNPP (reference structure). DNA carbon atoms are green. B, complex with template 8-oxoG paired to dCMPNPP. DNA carbon atoms are light blue except for 8-oxoG carbons that are highlighted in magenta. Arg-61 and the primer 3′-terminal T adopt two alternative conformations. C, complex with template 8-oxoG paired to dAMPNPP. DNA carbon atoms are lilac except for 8-oxoG carbons that are highlighted in pink. D, complex with template 8-oxoG paired to dGMPNPP. DNA carbon atoms are brown except for 8-oxoG carbons that are highlighted in purple.