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. 2017 Jan 20;45(5):2736–2745. doi: 10.1093/nar/gkw1363

Figure 2.

Figure 2.

Energy profiles for the pol β nucleotidyl transfer reaction. (A) Profile obtained from QM/MM calculations with either two (blue) or three (red) magnesium ions. The reaction coordinate is chosen to be the distance between the primer terminal nucleophile O3΄ and Pα of the incoming dCTP; the distance is reduced from right to left. In the designated transition state region (TS), the dissociating Pα–Oαβ bond has been stretched by 0.2 Å over its equilibrium distance. Also, the reactant (RS) and product states (PS) are indicated. (B) The starting (gray) and final (color) configurations of the QM sub-system (100 atoms) in the three magnesium calculation. Magnesium ions are represented by solid spheres (gray or green). All quantum waters are shown. Key water and Oαβ interactions in the final state are indicated with red dashed lines. (C) The starting and final configurations of the QM sub-system (99 atoms) with two magnesium ions. A water interaction with Oαβ in the final state is highlighted (red dashed line).