Figure 3.

Sequential representation of the evolution through the normal mode associated to the reaction coordinate for the deprotonation process in M3RA. For clarity, only the QM atoms are shown. The evolution of the Lys4(N)-H⁺ bond through the reaction normal mode is represented sequentially from (a–d). The concerted nature of the process is revealed involving three water molecules in the process. The second structure denoted as (b) TS corresponds to the geometry at the transition state of the reaction, where the surface corresponding to the DORI analysis is also included, which reveals the role of Tyr130 in the proper alignment of Lys4-H⁺ and the water channel. (enzyme’s carbon―orange; substrate and cofactor carbon―gray; red―oxygen; blue―nitrogen; white―hydrogen and the isovalue used as cutoff for the surface was defined at 0.5).