Roles of the Zinc Ion and Water Molecule in the Active Site of the Copper-Zinc SOD Catalyst

Abstract

In this work, we study the effect of a water molecule and a zinc ion on the catalytic activity of copper-zinc superoxide dismutase by computer simulation at the level of density functional theory using the PBE functional and the def2-SVPD and def2-TZVPD basis sets. Assessment is carried out in two directions. The first is a comparison of the main characteristics of electron transfer according to Marcus in the presence and absence of a water molecule in the active site. The second is the topological analysis of the electron density of the ligand environment of the copper ion according to Bader. It has been found that the presence of a water molecule and a zinc ion next to a copper ion has little effect on the primary stage of catalysis, the reduction of the copper ion. However, their presence significantly affects the course of the second stage of the catalytic cycle in the oxidation of copper. The water molecule is involved as a proton carrier. It may be present next to the copper ion during primary electron transfer. The water molecule leaves the first coordination sphere of copper after the initial electron transfer; otherwise, it forms a strong bond with the nitrogen atom, interrupting the electron transfer, according to the topological analysis. The presence of a water molecule near copper significantly impairs the secondary electron transfer, and the catalytic cycle is generally blocked.