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Many proteins or enzymes contain metal ions within their active sites.

These metals are often directly involved in the reaction catalysed bu the enzyme. In certain cases the function is well known and understood, including the identity of the metal and the changes in oxidation state throughout the reaction.

I wonder how the metal and oxidation state is determined a priori when a new structure is obtained. For examples if I solved a structure of a previously unknown enzyme by crystallography I may be able to determine that it contains Zinc (iron a better example), but knowing the density map tells me nothing about the oxidation state which may be important to function.

I think it must be possible to determine this, however I do not find much reliable information (inorganic complexes typically have other techniques in addition to X-ray). The situation is made harder as many protin structures in the pdb appear to be assigned without any real study.

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    $\begingroup$ No way there's Zn other then (II) in a protein - Fe would be a better example. $\endgroup$ – Mithoron Feb 19 at 22:35
  • $\begingroup$ Well, if your crystal is good enough, you know that the cell should be neutral and then you can basically count the charges. If you have multiple metal ions in there it becomes more difficult. $\endgroup$ – Martin - マーチン Feb 19 at 23:11
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X-ray diffraction experiments, regardless if about small molecules or proteins / RNA / DNA, are usually one element characterizing a sample. On occasion, you may infer the oxidation state from the transition metals environment: how many closest neighbors, their distance, their number, their spatial arrangement.

You are free to complement findings by any other technique either using the same crystal sample as mounted on the diffractometer (e.g., UV-Vis), or with sample material from the same batch characterized at the same temperature as the crystal mounted on the diffractometer: spin characterization by EPR, Moessbauer, NMR (your are not constrained to CHN) and SQUID to mention a selection. Because PubMed includes records about the structure characterization of large biomolecules, this database may serve as a source of inspiration how this was done, e.g., for heme

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