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Distances between specific residues during the MD simulations at pH 7.0 (A–C) and 4.0 (D–F). The abbreviations used for specific atoms are: NE2, histidine imidazole nitrogen; O2, terminal carboxylate oxygen; CO, backbone carbonyl oxygen; NH, backbone amide nitrogen; OD2, aspartate side-chain oxygen; NZ, lysine side-chain nitrogen; CM, center of mass of the tryptophan indole ring.
