Fig. 4: 8-oxodGTP insertion opposite C_t.

a Active site of the Ca²⁺-bound 8-oxodGTP(anti):C_t(anti) ground state (GS) ternary complex (PDB id 7KTA). Active site residues that interact with the incoming nucleotide or metals are shown. Ca²⁺ atoms are displayed as orange spheres. Protein side chains are shown in yellow stick, DNA is in cyan, and the incoming nucleotide is in green. Simulated annealing (F_o–F_c) omit density (green mesh) shown is contoured at 3.0 σ, carve radius 2.0 Å. b Top down close-up view of 8-oxodGTP(anti) interactions in the active site (PDB id 7KTA). 8-oxodG and template bases (yellow) are shown overlaid with the Ca²⁺:dGTP(anti):C_t(anti) ground state complex (green). Arrows indicate differences in the positions of dGTP and 8-oxodGTP. Hydrogen bonding for 8-oxodGTP is shown with black dashes and distances (Å) are labeled. Clashes are shown with red dashes. c Active site of the Mn²⁺-reaction state (RS) ternary complex of pol μ inserting 8-oxodGTP(anti) opposite C_t (PDB id 7KTB). Ca²⁺:8-oxodGTP:C_t ternary complex crystals were soaked in a Mn²⁺-containing cryo solution for 40 min. Arrows indicate bond broken (substrate) and formed (product). Mn²⁺ atoms are purple spheres. d Active site metal coordination in the RS complex (PDB id 7KTB). Coordination is shown with dashes and distances (Å) are labeled. Water molecules are shown as blue spheres. Anomalous density (magenta surface) is contoured at 5 σ. e Comparison of the locations of Mn_p,8-oxodGTP (purple) (PDB id 7KTB), Mn_p,dGTP (pink) (PDB id 7KSU), and Mn_p,TTP (magenta) (PDB id 5TYX) displayed overlaid on the Mn²⁺:8-oxodGTP(anti):C_t(anti) reaction state ternary complex (PDB id 7KTB). Red dashes indicate distances between metal ions. f Comparison of Mn_p,8-oxodGTP (purple) (PDB id 7KTB), Mn_p,dGTP (magenta) (PDB id 7KSU), and Mn_p,TTP (pink) (PDB id 5TYX) coordination by the incorporated phosphate (P_n+1) and phosphate oxygen of PP_i in the 8-oxodGTP(anti):C_t(anti) reaction state ternary complex (PDB id 7KTB, 8-oxodGTP not shown for clarity). Coordination distances (Å) are shown with black dashes for Mn_p,8OG and with grey dashes for Mn_p,dGTP and M_np,TTP. g Active site of the product state of the 8-oxodGTP(anti):C_t(anti) insertion (PDB id 7KTC). Ground state ternary complex crystals were soaked in a Mn²⁺-containing cryo solution for 120 min.