Stability of Zn binding sites in MD simulations of YiiP. The RMSD of binding site residues, represented by their nonhydrogen atoms in the backbone and side chain, was calculated after optimal superposition of each protomer for apo and holo simulations and each simulation repeat (md0–md2), shown in shades of purple and cyan, respectively. To improve readability, the time series was averaged over blocks of 20 ns with the solid line showing the mean and the error band containing 95% of the data. RMSD distributions generated by a KDE are shown to the right of the time series. On the far right, each binding site in the SP3sym structure is shown with the Zn ion (magenta sphere) and the coordinating residues (licorice representation). (A) Site A in the TMD. (B) Site B in the M2/M3 loop of the TMD. (C) Site C2 in the CTD. (D) Site C1 in the CTD.
