You can find instructions for restraining Zn-ligand distances here:
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement&highlight=metal%20ion#Restraining_metal_ligand_distances_during_refinement_in_REFMAC
Using this method, only Zn-ligand bond distances are restrained. REFMAC
can usually find on its own certain Zn-atom linkages (I think it can
find ZN-SG bonds with Cys by itself, but the version I am using usually
misses or ZN-OD1 or ZN-OD2 bonds with Asp. This I pick up in the .cif
file generated by REFMAC and include in a library file to be used for
refinement. I have not had any issues with REFMAC altering ZN geometry.
What you describe sounds like the geometry of the ZN atom has been
defined or assumed somewhere in your approach.
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
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Hamilton, NY 13346
tel: (315)-228-7245
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email: [email protected]
On 6/6/2013 10:36 AM, James Naismith wrote:
I have a structure that I am trying to finish off, I have Zn ligated by four
cys residues.
I use the linkR and define distances (the same link for each ZnS bond)
My issue is how to stop the structure moving to a square pyramid (consistent
with distance restraints) rather than a tetrahedral geometry.
Can anyone help?
best
Jim
Jim Naismith
BSRC, North Haugh
[email protected]
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