It has been proposed that the metal ion will bind to the core structure of my protein, previous work had added this metal ion during the overexpression and purification procedures for the catalytic activity of this enzyme. Meanwhile, I will be working on the X-ray structure of that enzyme, will the metal ions show in the result when I diffract my crystal? Or I still need to dock for the ions binding site?
Thank you.
Depends on the occupancy of your metal binding sites - if you retain high enough occupancy (high affinity sites), you will see the metal ions, if you have low occupancy, possibly paired with high disorder, you might not get a sufficiently high signal in the electron density map to discern the sites from background noise. Addition of metal ions ensures a high occupancy of the genuine metal binding sites, but may also light up some spurious low affinity sites that may not be occupied under physiological conditions.
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