Figure 9
(A) The structure of the N-acetylmuramic acid-D-Ala (NAM-D-Ala) molecule used in molecular docking. (B) Surface representation of the complex and the positioning of the NAM-D-Ala in the binding site of EfAmi1. (C) Ribbon representation of EfAmi1 structure with the NAM-D-Ala bound. The Zn2+ ion is shown as a purple sphere. (D) A detailed transparent view of the interaction between NAM-D-Ala and the amidase-2 domain (gold). The side chains of selected residues (blue) are shown in stick representation and labelled. The Zn2+ ion is shown as a purple sphere. (E) 2D representation of the interactions of EfAmi1 amidase-2 structure with the docked NAM-D-Ala molecule using the LigPlot + v.2.255.
