Ion replacement in protein active site is attracting considerable interest due to its application in some spectroscopic methods like perturbed angular correlation. Theoretical consideration of ion replacement in plastocyanin was done using the two layer ONIOM method. The copper (I) and copper (II) ions in the plastocyanin active site were replaced by silver (I) and cadmium (II), respectively. Optimization of the four proteins was done with LANL2DZ and SDD basis sets. Molecular orbital, natural bond orbital and atom in molecule analysis were used to determine the electronic structures of the four active sites. The total energy of copper (I) plastocyanin is lower than that of silver (I) plastocyanin. Copper (II) plastocyanin showed a lower energy than cadimum(II) plastocyanin. HOMO and LUMO orbital energies of the copper (I) and cadmium (II) active sites are lower than those of the silver (I) and copper (II) active sites, respectively. The four active sites displayed different charge distribution. Atom in molecule theory demonstrated different values for electronic density and bond ellipticity for the four active sites.

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