Equilibrium binding analyses were performed in this study to assess the influence of pH value, salt concentrations, and number of exposed histidine residues of protein on the binding affinity and capacity of imidazole and proteins to immobilized Cu(II) ion. The proteins under investigation were lysozyme, ribonuclease A, and hemoglobin, with the number of exposed histidine residues being 1, 2, and 27, respectively. Molecular modeling estimation was also performed to reveal the solvent-accessible surface area of each histidine residue. Also, the results obtained from the calculations on the number of exposed histidines of the proteins were found to be compatible with those in the literature. Moreover, the impact of the pH value on the binding affinity and capacity of imidazole and proteins to immobilized metal ion were described by the deprotonation of N-imidazole and close proximity of adsorbed imidazole on immobilized metal ion gel. However, the variation of binding capacities with salt concentration indicated the existence of a manifold binding mechanism involving hydrophobic and electrostatic interactions of solutes with immobilized Cu(II) ions and with the hydrophilic gel surface. Moreover, the different responses of the proteins toward the effects of pH values and salt concentrations were interpreted by the specific features of the protein surface structure and by the different expressions in the adsorption isotherm.