Thanks for this other suggestions similar (see below.)
My problem is not the distances per se, these restrain fine to 2.3A
I am relatively low resolution and my problem is with just distance restraints I move to a square planar arrangement. I suspect this is a feature of the geometry restraints dominating refinement (c'est la vie at low res).
I do not force Zn to be anything (the cif file just has a distance) I think.
What I need to do is create another restraint someone how that imposes a Td geometry.
What I cannot figure how to do is set this up because it involves 5 residues (4 cys and 1 Zn).
best
Jim
Jim Naismith
BSRC, North Haugh
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On 6 Jun 2013, at 16:11, Roger Rowlett <[log in to unmask]> wrote:
> 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
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>
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> 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
>> [log in to unmask]
>>
>> Google scholar is free and tracks your outputs, mine are
>> http://scholar.google.co.uk/citations?hl=en&user=fLmKKQMAAAAJ
>>
>> ResearcherID H-3408-2012; SCOPUS_ID 7005691850
>>
>> http://www.researchgate.net/profile/James_Naismith/
>>
>> The University of St Andrews is a charity registered in Scotland : No SC013532k
>
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