The role of zinc ion in the active site of copper-zinc superoxide dismutase

Abstract

The interaction of the superoxide radical ion O2– with the active site of Cu, Zn-superoxide dismutase was studied by computer simulation using the ORCA software package version 5.0.2 at the level of density functional theory using the PBE functional and the basis sets of functions def2-SVP, def2-SVPD and def2-TZVPD. The main characteristics for two processes of electron transfer in the catalytic cycle of radical ion deactivation were obtained: reaction potential ΔG0, total reorganization energy λtot, activation energy ΔG≠, overlap matrix element HDA, and transfer rate constant k according to Marcus. The variable factor in the modeling was the presence of the Zn2+ ion in the active site of the enzyme. Two variants of the electron transfer mechanism were considered: one carried out with the help of ligands and another occurring in the immediate vicinity of an oxygen-containing particle and a copper ion. It has been established that the presence of the Zn2+ ion contributes to a large extent only to the second electron transfer from the Cu+ ion to the protonated form of the radical ion, to the hydroperoxide radical HO2. Other things being equal, the zinc ion increases the electron transfer rate constant by five times through specific interactions.