Re: [ccp4bb] How do CNS deal with the His NE2 atoms coordinated with Zn2+?

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: How do CNS deal with the His NE2 atoms coordinated with Zn2+?
From: Deqiang Yao dqyao {- at -} CRYST {- dot -} IPHY {- dot -} AC {- dot -} CN
Date: 2007-04-26

Next message:
Subject: Re: R and Rfree
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-26

Subject: Re: How do CNS deal with the His NE2 atoms coordinated with Zn2+?
From: David Briggs bassophile {- at -} GMAIL {- dot -} COM
Date: 2007-04-26

Hi there.

1) ensure you have the right name/atom descriptor for zinc in CNS in
your zincs.pdb for the generate script
Residue name > ZN2
Atom name > ZN+2
Type > ZN+2
(you can check these by searching though the ion.top file)

2) Use refmac. I find it is easier to decode what is going wrong with refmac.
CNS logs can be a little impenetrable. Refmac has done a fine job of
the Zinc binding proteins I've played with.

Hope this helps,

Dave

On 26/04/07, Deqiang Yao wrote:
>
>
>
> Help someone ask a question.
>
> * How do CNS deal with the His NE2 atoms coordinated with Zn2+?
>
> Dear all:
> we have a crystal structure with a Zn2+ tetrahedron coordinated by
> three His NE2 atoms and one water.
> Is the proper coordinating distance between three His NE2 atoms and Zn2+ ion
> is in the range from 1.95-2.1A?
> But we have not get this result by CNS refinement with parameter_infile
> 'protein_rep.param and ion.param'.
> We think that the His NE2 atoms are non-protonated when coordinated with
> Zn2+, differ from the free His residues.
> But we don't know how CNS deal with the His NE2 atoms coordinated with Zn2+.
> How can we get the right coordinating distance?
>
> Any help is welcome!
> Best regards,
>
> Deqiang Yao
>

--
---------------------------------------
David Briggs, PhD.
Father & Crystallographer
www.dbriggs.talktalk.net
iChat AIM ID: DBassophile
---------------------------------------
Anyone who is capable of getting themselves made President should on
no account be allowed to do the job. - Douglas Adams

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: How do CNS deal with the His NE2 atoms coordinated with Zn2+?
From: Deqiang Yao dqyao {- at -} CRYST {- dot -} IPHY {- dot -} AC {- dot -} CN
Date: 2007-04-26

Next message:
Subject: Re: R and Rfree
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-04-26