The metal dissociation constants of bovine carbonic anhydrase II, bovine carboxypeptidase A, rat aminopeptidase B, and rat dipeptidyl peptidase III were measured using metal buffer solutions. The zinc dissociation constants of bovine carbonic anhydrase II, bovine carboxypeptidase A, rat aminopeptidase B, and rat dipeptidyl peptidase III were 5.8×10(-14), 3.5×10(-12), 3.7×10(-13), and 1.9×10(-13) M, respectively. The ternary complex between metal derivatives of bovine carbonic anhydrase and various chelating agents were characterized using the kinetic method and visible and magnetic circular dichroism spectra. The coordination geometry of the ternary complex was in the equilibrium state between the five and the tetrahedral coordination geometry. The equilibrium state depends on the character of ligands. Dipeptidyl peptidase III which has an abnormal zinc binding motif (HEXXXH) was characterized using the point mutation and computer simulation methods. The abnormal zinc binding motif (HEXXXH) of rat dipeptidyl peptidase III has a large helix part. It is generally known that the cupric derivatives of the zinc peptidase loses enzyme activity, but the cupric derivative of dipeptidyl peptidase III surprisingly has enzyme activity. The measurement of the electron paramagnetic resonance spectra of the cupric rat dipeptidyl peptidase III in the presence of the substrate showed that the coordination geometry is very flexible. The flexibility of the coordination geometry in the cupric rat dipeptidyl peptidase III is important for the expression of enzyme activity. Docking simulation was used to identify the substrate binding site of aminopeptidase B, which is a powerful tool to estimate substrate binding residues in enzymes.