Well, when I solved a structure for a protein-rhenium adduct I had to
manually code a restraint file for the rhenium tricarbonyl fragment,
which is octahedral overall (with proteins ligands and waters), and had
several different types of bond distances for the various ligands. I
started with an incorrect description of a similar ligand cif file from
HIC-UP and hand-edited the cif file to suit. It seems to me it should be
possible (although somewhat painful) to write a similar restraint file
(geometry + bond lengths) for ZN.
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [log in to unmask]
On 6/7/2013 9:23 AM, Tim Gruene wrote:
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> Hi Jim,
>
> the chemical basis would be that the Zn connects to all four S atoms,
> and if they are indistinguishable, all Zn-S distances should be alike.
>
> But the S-atoms are not bonded to each other, hence they want to have as
> much distance from each other as possible. Since they are four, this
> makes them a tetrahedron.
>
> I am not aware of a more automated/ simpler way of turning the angles
> at the metal into restraints other than calculating the S-S distances
> with a pocket calculator, although that does not mean they do not exist.
>
> Cheers,
> Tim
>
> On 06/07/2013 11:56 AM, James Naismith wrote:
>> Andrew Leslie made a similar suggestion for using CB to S
>> distances.
>>
>> Both make me unhappy for the reason that there is not a clear
>> chemical basis to them (Tim's has more a chemical basis) and how
>> would I choose the distance. (I can measure it from a known
>> structure)
>>
>>
>> I have previously experimented with Tim's (works). I am searching
>> for anyone who knew a simple way to restrain metal ion geometry in
>> remfac based on angles at metal.
>>
>> best Jim
>>
>>
>>
>>
>>
>>
>>
>>
>> On 7 Jun 2013, at 10:14, Tim Gruene <[log in to unmask]>
>> wrote:
>>
>> Dear James,
>>
>> I am not sure I fully picture what your coordination looks like,
>> but my guess is that if you include distance restraints between the
>> S-atoms you can distinguish between a tetrahedral geometry and a
>> square pyramid.
>>
>> You could use external restraints in refmac - just make a dummy
>> run with prosmat to get the syntax right and copy and modify a few
>> lines tailored to your problem.
>>
>> Best, Tim
>>
>> On 06/07/2013 10:39 AM, James Naismith wrote:
>>>>> 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 [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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 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
>>>>>> Colgate University 13 Oak Drive Hamilton, NY 13346
>>>>>>
>>>>>> tel: (315)-228-7245 ofc: (315)-228-7395 fax:
>>>>>> (315)-228-7935 email: [log in to unmask]
>>>>>>
>>>>>> 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
>>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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