Fig. 7: High mobility of Mg⁺² at site A*.

a Electrostatic surface potential of the dNTP binding site. Graphical surface representation of the charged cavities colored by the electrostatic potential for RT-T/P binary complex (left), state R-1 of RT-T/P-dATP (center), and RT-T/P-dATP 3′ chain terminated (right). A negatively charged pocket is formed upon dATP binding (yellow arrows). Pockets were detected using a 4 Å cavity detection radius and a 4 Å solvent radius cavity detection cutoff in Pymol. Protein backbone is shown in cartoon representation with key residues displayed in ball-and-stick representation. b Superposition of all states (left panel) reported in this study showing that site A* Mg²⁺ has high mobility, while the position of site B Mg²⁺ had minor changes in all experiments. Dash green circle corresponds to site A in P_6min. Right panel, overlay of the 3′OH chain terminated structure (violet) with the T_8sec structure shows that the Mg²⁺ ion shifts from the A* to the canonical A position (dash arrow) in the absence of a 3′OH group, with concomitant D185 residue rearrangement (solid arrow).