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Figure 7
Time evolution of the Ile257 residue in each monomer of the AcNiR trimer during MD simulations. (a) The distance between the sterically important Ile257 residue side-chain CD1 atom and the type 2 Cu atom is shown for the protonated Asp98p (blue) and deprotonated Asp98 (green) states of the protein. In Asp98p, the Ile257 CD1 side-chain atom is preferentially oriented towards the type 2 Cu atom in conformation II, compressing the space between them and in a position that would impose limits on ligand selectivity and binding geometry at the active site. In its deprotonated Asp98 state, Ile257 is predominantly found in the conformation I position, although fluctuations between conformations I and II may also occur, as seen around ∼20 ns for monomer B of the AcNiR trimer (middle panel). (b) shows the position of Ile257 in conformation I (right) and conformation II (left) overlaid with the crystal structure. In (b), the MD conformation is shown in ball-and-stick representation and the crystal structure by thin lines. The two conformations of Ile257 in conformations I and II are shown in thicker green and blue lines, respectively.

IUCrJ
Volume 4| Part 4| July 2017| Pages 495-505
ISSN: 2052-2525
https://doi.org/10.1107/S2052252517007527