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. 2020 Jan 11;118(5):1221–1233. doi: 10.1016/j.bpj.2019.12.035

Figure 4.

Figure 4

Binding in DimerM. (A–C) Schematic representations of the binding sites Zn1 (with H193) and Zn2 (with H140) obtained in the MD simulations are shown. The coordination pattern is found (A) in three (MD simulations 2, 3 and 4 in Table S2), (B) in one (MD 5 in Table S2), and (C) in one simulation (MD 1 in Table S2). The white circles represent water molecules. (D) A snapshot from one MD simulation showing the most frequent binding situation (A on the left) is given. (E) Time evolution of all the H140(Nε)-Zn and H193(Nε)-Zn distances in all five MD simulations is shown. 20 distances are plotted and are stable around 2.1 Å. Only one of the 10 H193-Zn interactions is lost but simultaneously replaced by a water-mediated interaction, shown in red in (E) and as a white circle with an arrow in (B).