Fig. 4: Structure of human PrimPol extending from an incorrect primer A base opposite the oxoG template base.

a The overall structure of the ternary PrimPol oxoG•A extension complex (molecule A of the asymmetric unit, AU). 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, the two Ca²⁺ ions (metals ‘A’ and ‘B’) are shown as light blue spheres. The oxoG residue (orange) is forming a base pair with the primer terminal A base (purple). The incoming dATP forms a nascent base pair with a template T base, which is 5′-adjacent to the oxoG residue. 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 3′-deoxy primer C14 base in the PrimPol active site (molecule A in the AU). Two Ca²⁺ ions (metals ‘A’ and ‘B’) in this complex shown as light blue spheres, and the water molecule coordinated by the Ca²⁺ ion is shown as a small red sphere. c A simulated annealing Fo−Fc omit map (contoured at 2.5σ-level at 2.07 Å resolution and colored in blue) showing the clear electron density for the oxoG residue in the syn conformation and its partner A14 residue in molecule B of the AU. The water molecule that facilitates the intramolelecular bond between the N² and the phosphate group of the oxoG residue is observed only in molecule B. d A simulated annealing Fo−Fc omit map (contoured at 2.5σ-level) showing the electron density for the oxoG(syn) and its partner A14 residues in molecule A of the AU. There is only one hydrogen bond in this base pair. e Similar phosphate backbone conformations of T3-oxoG4(syn)-C5 (gray and orange) and unmodified T3-C4-G5 (beige) template strand segments within the PrimPol active site of their respective ternary complexes. The main-chain nitrogen atom of Gln48 and the side chain of Arg47 contact the phosphate group of the oxoG(syn) similarly to the protein contacts with the phosphate group of C4 in the unmodified complex.