Fig. 2.

Coordination of the Na⁺ at the Na2 site. (A–F) The distance between the Na⁺ at the Na2 site and each residue shown was measured when only the Na2 site was occupied (blue), Na2 and Na1 were occupied (red), or Na2, Na1, and I⁻ were all occupied (black). The x axis represents the distance between the Na⁺ and the atom in the residue closest to it. The y axis represents the fraction of the 5,000 frames in which the Na⁺ at the Na2 site was found at the indicated distance from the indicated residue. Each Inset shows two distances between the Na⁺ at the Na2 site and the side-chain oxygen when the three ions were present (black line). For Q263, only one distance is shown, corresponding to the observed single peak. Each Inset also shows the position of S353. (G) Summary of the integrated frequencies and free energies of residues 0–3 Å from the Na⁺ at the Na2 site. (H) Summary of the integrated frequencies and free energies of residues 3–5 Å from the Na⁺ at the Na2 site.