Fig. 3.

Deprotonation of the 3′-OH. (a) Superposition of the refined RS (80s, yellow) and PS (300s, blue). The transient water molecule, likely deprotonating the 3′-OH, is circled. The sugar pucker at the primer 3′-end changes from C2′-endo in the RS to C3′-endo in the PS. The clashes between the α-phosphate and the C2′ if it is C2′-endo, and between the C2′ and the transient water if the water doesn’t depart, are indicated by dashed double arrowheads. (b) WT and S113A mutant hPol η can both extend primer with a ribonucleotide at the 3′end (lighter color) as with pure DNA (darker color).