The biological CuA site functions as the proximate electron-transfer intermediate from an electron source in cytochrome c oxidase and nitrous oxide reductase. It provides a characteristic electronic structure for rapid electron transfer. In the CuA site, two copper ions bridged with two bridging cysteinyl thiolate groups form an almost planar Cu2S2 core. Each copper ion is coordinated equatorially with a histidine residue and axially with either a methionine residue or a carbonyl group of the polypeptide backbone. Three-dimensional X-ray crystallographic structures show that the structural variety of the Cu2S2 core of the CuA site with a short CuCu distance of 2.34–2.59 Å and a SS distance of 3.76–4.24 Å. In the present study, we address the origin of the structural variety of the Cu2S2 core of the CuA site, using the density functional theory. Our computation demonstrated that we found the structural dependence of the energy gap between the σ and πu oxidized states, the ionization potentials, and total energies, though the structural variety is insensitive to the shape and symmetry of the σ and πu redox active molecular orbitals and the πu ground state of the Cu2S2 core of the CuA site. In addition, the σ oxidized state is more robust to the structural changes in ionization potentials and total energies than the πu oxidized state. This robustness indicates the small reorganization energy in the redox reaction between σ oxidized and reduced states of the CuA site. The optimized Cu2S2 cores have almost same structures in all the states, indicating that surrounding proteins are responsible for the structural variety of the Cu2S2 core of the CuA site. © 2012 Wiley Periodicals, Inc.