FIGURE 4.

Comparison of the active sites in V. alginolyticus PepD and structural homologs. A, local view of the di-zinc center of PepD. The residues involved in coordination of Zn1 and Zn2 (gray spheres) are shown as green sticks. B, local view of the di-zinc center of PepV. The residues involved in metal coordination are shown as cyan sticks, and the phosphinic inhibitor (AspΨ[PO₂CH₂]AlaOH) is represented by yellow sticks. In the PepD active site, Zn1 is coordinated by Asp¹¹⁹, His⁴⁶¹, and a single putative water molecule hydrogen-bonded to the Glu¹⁴⁹, whereas Zn2 is coordinated by His⁸⁰, Asp¹¹⁹, and Asp¹⁷³. The putative water molecule of PepD is depicted by a red dot. Asp¹¹⁹ of PepD serves as a bridging ligand for metal coordination.