Figure 5.

Structural comparison between reactant states of incorrect nucleotide incorporation during dN or rN extension show increased inclination of primer terminus alignment during rA or rU extension misincorporation. A,C, structure of rA extension (A) and rU extension (C) WT Pol η mismatch reactant state complexed with Mg²⁺. B, D, structural overlay of dN (green) (PDB ID 4J9M and 4J9K) or rN (pink) extension structures with dGMPNPP:dT base-pair indicating differences in 3′-OH alignment. The misaligned primer terminus in the dN structure (green) is colored with yellow green. All electron density maps apply to the molecule colored in pink. The 2F_o-F_c map for everything including Me²⁺_A and Me²⁺_B, dGMPNPP, and catalytic residues and S113 (blue) was contoured at 2 σ. The F_o-F_c omit map for the primer terminus (green) was contoured at 3.5 σ in A, B, and 2.7 σ in C, D. rU, ribose uridine; dN, deoxynucleotide; Pol η, DNA polymerase η; rN, ribonucleotide; dT, deoxyribose thymine.