Fig. 3: 8-oxo-rGTP(anti) insertion opposite cytosine.

a Active site of the reaction state ternary complex of the 8-oxo-rGTP(anti):C_t insertion after an overnight soak (960 min) in a Mn²⁺-containing cryo-solution. Arrows indicate bond broken (substrate) and formed (product). Protein sidechains are shown in yellow stick representation, nucleotide in green and DNA in cyan. Mn²⁺ is shown as a magenta sphere. Simulated annealing (F_o–F_c) omit density (green mesh) is shown at 3 σ. b Top down close up view of nucleotide and possible product metal (Mn_p,8rOG, purple sphere) interactions in the ribo-8-oxo-GMP(anti)/GTP:C_t active site. Shown is an overlay with the deoxy-8-oxo-GTP(anti)/GMP(anti):C_t Mn²⁺-reaction state ternary complex in magenta. The product metal in the latter structure (Mn_p,8dOG) is shown as a magenta sphere. Mn_p,8rOG bridges O8, an oxygen of the phosphate of the incorporated nucleotide and an oxygen of PP_i. Hydrogen bonding and other key distances (Å) are shown with black dashes. Red spheres indicate (unfavorable) destabilizing interactions. Inset. Comparison of Mn_p,8rOG and Mn_p,8dOG coordination of O8 and product phosphate oxygens. A black arrow indicates differences in the position of O8. c Mn²⁺-product complex of the 8-oxo-rGTP(anti):C_t insertion. Simulated annealing omit density is shown as a green mesh contoured at 3 σ. d Contributions of selected protein and nucleic acid residues to the interaction free energy of 8-oxo-rGTP in the unreactive (light orange) and reacted (red) conformations within the Mn²⁺-reaction state ternary complex of the 8-oxo-rGTP:C_t insertion (see Supplementary Tables 6, 7). C_t (template nucleotide), T_n-1 (opposite P_n-1 in template strand), P_n-1 (primer strand), and P_n (primer terminal nucleotide) represent selected nucleotides in the template or primer strands.