FIGURE 4.
Substrate binding poses in the Sc site of vSGLT and PutP. A, distribution of the probabilities of finding the galactose molecule at a given position in the Sc site of vSGLT (expressed in a spherical coordinate (r, θ, ϕ) and using the coordinate to Na2 as the reference point, see Fig. 3). The galactose binding poses are divided into three clusters based on this distribution. B, average MM/GBSA energies of each the galactose pose cluster in the Sc site. Corresponding results for PutP are shown in C and D. The substrate binding poses in the Sc sites of vSGLT (E) and PutP (F) are represented by vectors (from the center of the ring pointing toward the carbons outside the rings for both galactose and proline). In addition to the gating residues Tyr-263 of vSGLT and Tyr-248 of PutP, residues that were experimentally tested are shown as sticks. The Se-bound substrates are in sphere representations.