Dave, Others have given many excellent suggestions :) I'd like to mention that to a protein biochemist such as myself, another obvious solution would be to take an aliquot of the protein for a metal analysis (via ICP or AA). ICP is more sensitive. Both Mn and Ca will light up the spectrum like new year's tree lights.
Artem > The obvious solution is go to a synchrotron and scan around the Mn edge > and > see what happens, however, whilst waiting for beam time, is there any way