Figure 7.

Alternative conformations of the loop region in the (a) first, (b) second, (c) third, and (d) fourth modes for the asymmetric mixed cg TIM-PGH complex are displayed. The loop region (166–176) in red/yellow, one PGH molecule, and the neighboring segments of the loop region (blue/gray) are indicated. The important residues and side chains are also indicated. Other residues are shown as light gray lines in the background to indicate the perspective. In general, mixed cg calculations agree with the experimental findings, indicating that the tip of the loop 6 (α carbon of Thr172) is displaced more than 7 Å between the open and closed conformations, the catalytic base Glu165 moves about 2 Å to force the ligand in a planar conformation for catalysis, the amide group of Gly171 makes a hydrogen bond with the phosphate group of the ligand in the closed conformation, and the indole ring of Trp168 rotates about 50° upon binding.