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. 2015 Mar 24;108(6):1390–1399. doi: 10.1016/j.bpj.2015.02.010

Figure 5.

Figure 5

Substrate and ion binding sites and release. (A) Substrate and ion binding sites for the outward- and inward-facing state of LeuT. The structure of the outward-occluded conformation of LeuT (PDB: 2A65 (6)) is shown in darker colors and the structure of the inward-open conformation (PDB: 3TT3 (24)) is shown in lighter colors. TM1 (red) and the residues surrounding the substrate and ion binding sites are shown (sticks colored according to element with the carbon atoms in cyan). The substrate bound in the outward-occluded conformation is shown (sticks colored according to element with the carbon atoms in orange and the two Na+ ions are shown as yellow spheres). (B) Plot of position relative to the starting position for the two Na+ ions initially bound in the Na1 and Na2 site and the center of mass of alanine. (C) Plot of occupancy of each of the two Na+ ion binding sites during the ALA simulations. To see this figure in color, go online.