You can have a look at the following paper, it may be helpful:

J. Spiriti, A. van der Vaart, Mechanism of the Calcium-Induced trans-cis Isomerization of a Non-Prolyl Peptide Bond in Clostridium histolyticum Collagenase, Biochemistry 49(25):5314-20, 2010.

It depends on what you want to do.Compute binding equilibrium in solution?What kind

of ion?Whatt pH?Are there other ions present?More than one candidatesite on the protein?Is the protein structure known?Do you want to do QM computation?If you just model with standard empirical force fields,try to find a similar local environment in the

 PDB with a bound cation  in it  use the distances plus the energy parameters in the force field you are using and you get  a (very rough) estimate of the binding energy..if

you want to estimate the binding equilibrium in solution this is of course much more difficult  because you must  know either from theory or experiments the chemical potentials of all components involved (water,other ions etc) and consider solvation desolvation free energies and coulomb fields acting on your site.Alternatively try to find good experimental data..