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. Author manuscript; available in PMC: 2018 Apr 15.
Published in final edited form as: Virus Res. 2017 Jan 16;234:135–152. doi: 10.1016/j.virusres.2017.01.006

Figure 5. Phosphodiester bond formation.

Figure 5

The substrate NTPs (D1 and D2) that would form the first two bases of the daughter chain are paired with the two bases (T1 and T2) at the 3′-end of the template. This priming platform is stabilized by Y630 from the C-terminal domain that base stacks with D1. The nucleotidyl-transfer reaction requires two Mg2+ ions - one (MgA) that coordinates the 3′-OH of NTP D1 and the a-phosphate of the NTP D2; a second (MgB) that coordinates the β- and γ-phosphates of NTP D2 in addition to the sidechains of the conserved motif A (D324) and motif C (D453) aspartates. Coordination with MgA lowers the pKa of the 3′-OH of NTP D1 enabling a nucleophilic attack on the a-phosphate of D2 creating a phosphodiester bond between the two NTPs. The pyrophosphate product is stabilized by MgB. The nucleotidyl-transfer reaction is shown schematically in the lower panel.