Fig. 1: Structure of human PrimPol inserting correct dCTP opposite the oxoG template base.

a The overall structure of the ternary PrimPol oxoG•dCTP complex (molecule A complex in the asymmetric unit (AU) with the ordered N-helix). The N-helix and modules ModN and ModC are shown in cartoon representation in dark blue, yellow, and cyan, respectively. The DNA is shown as gray sticks, and the Ca²⁺ ion (‘metal B’) is shown as a light blue sphere. The oxoG residue (orange) is forming a nascent base pair with the incoming dCTP (red). The unstructured regions in the ModN and ModC modules are shown as dashed yellow and cyan lines, respectively. The side chains of key catalytic active-site residues Asp114, Glu116, and Asp280 are shown as red sticks. b A close-up view of the oxoG template base and the dCTP in the PrimPol active site. The key catalytic residues (Asp114, Glu116, and Asp280), the residues contacting the incoming dCTP (Lys165, Ser167, His169, Arg288, Asn289, Phe290, Arg291, and Lys297), the template oxoG base (Gly74, Gln75, and Arg76), and the rest of the template strand (Lys10, His46, and Arg47) are shown in sticks and with oxygen atoms in bright red and nitrogen atoms in blue. c A simulated annealing Fo−Fc omit map (contoured at 2.5σ-level at 2.60 Å resolution and colored in blue) showing the clear electron density for the entire oxoG residue in the anti conformation, its partner incoming dCTP, and the Ca²⁺ ion. Hydrogen bonds are indicated by black dashes. d Comparison of the phosphate backbone conformations of C2-oxoG3(anti)-C4 (gray and orange) and unmodified C2-T3-C4 (beige) template strand segments within the PrimPol active site of their respective ternary complexes. The complexes are superimposed by ModN and ModC of PrimPol protein. The oxygen atoms of the sugar-phosphate backbone and the O8 of the oxoG residue are colored in red. The phosphate group of the oxoG3(anti) residue is shifted by ~1.5 Å compared to the position occupied by the phosphate group of T3 residue.