Figure 2. Structures and Intermolecular Contact Details of Dpo4 Complexes with oxoG-Modified Template-Primer DNA.

(A) Schematic of the pairing of the oxoG-containing 19-mer template strand with the 13-mer primer strand ending in a 2′,3′-dideoxynucleotide in the preinsertion binary complex with Dpo4.

(B) Schematic of the pairing of the oxoG-containing 19-mer template strand with the 13-mer primer strand ending in a 2′,3′-dideoxynucleotide plus incoming dCTP in the insertion ternary complex with Dpo4. dCTP is positioned opposite oxoG.

(C) Schematic of the pairing of the oxoG-containing 19-mer template strand with the 14-mer primer strand ending in a 2′,3′-dideoxynucleotide in the postinsertion binary complex with Dpo4. Covalently incorporated C is positioned opposite oxoG.

(D) Structure of the active site of the preinsertion binary complex. The DNA and protein are in stick and ribbon representations, respectively. Template residues 1–6 (including oxoG) of single-stranded overhang are disordered in the electron density maps.

(E) Structure of the active site of the insertion ternary complex, with incoming dCTP paired with oxoG(anti) at the active site.

(F) Structure of the active site of the postinsertion binary complex, with covalently incorporated C paired with oxoG(anti).

(G) Details of the intermolecular contacts in the structure of the preinsertion binary complex.

(H) Details of the intermolecular contacts in the structure of the insertion ternary complex.

(I) Details of the intermolecular contacts in the structure of the postinsertion binary complex.

Color-coding for panels G–I. DNA-backbone phosphate groups interacting with the palm domain are shown in light green, the phosphate groups interacting with the thumb domain within the minor groove are shown in red, and the phosphate groups interacting with the little-finger domain within the major groove are shown in purple. The conserved interactions are boxed for the thumb and little-finger contacts.

Dpo4 amino acids interacting via the peptide backbone are labeled black, via their side chains, green, and via the backbone and side chains, orange. Black arrows indicate hydrogen bonding, blue arrows water-bridged contacts, and pink arrows depict van-der-Waals contacts.