[phenixbb] Protonation of a symmetry-related His in Zn coordination sphere

Priit Eek priit.eek at gmail.com
Fri Nov 16 02:34:36 PST 2018


I have a structure in which one of the His-residues of a Zn coordination sphere is from a symmetry-related protein chain. I specified the symmetry in an edits file so the coordination sphere is nice and plays well in refinement.

I now added hydrogens to the model, but the His from the other chain does not get protonated correctly. I assume reduce doesn’t detect the presence of the symmetry-related Zn. It protonates NE, while that is the atom that interacts with Zn, but ND should be protonated instead. What would be the best way to fix this?

And another question on the same matter: is it possible to specify a LINK in PDB between these atoms?

Best regards,



Priit Eek, PhD
Department of Chemistry and Biotechnology
Tallinn University of Technology
Tel. +372 620 4387
priit.eek at taltech.ee

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