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

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CCP4bb <-- 2007 <-- April 2007 <-- 26 April 2007

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From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
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Subject: Re: How do CNS deal with the His NE2 atoms coordinated with Zn2+?
From: Marius Schmidt marius {- dot -} schmidt {- at -} PH {- dot -} TUM {- dot -} DE
Date: 2007-04-26

It seems to me you have not patched the zinc to
the histidines.
there are two ways to attack this problem
1.) the proper way
in a topology file define a patch residue
PRES hiszc
bond 1NE2 2ZN
END

in a parameter file set restraint and distance
bond NE2 ZN 100.0 1.9
for an unrestrained refinement set the restraint to
small values (10.0)

in generate.inp patch 3 His residues to ZN
eg:
patch hiszc
reference=1= (resid 59) /* your histidine resid */
reference=2= (resid 180) /* your zinc resid */
end

repeat entry with the next his
patch hiszc
reference = 1 = (resid 65) /* resid of the next histidine */
reference = 2 = (resid 180)
end

until all his are patched to the zn.

generate, refine, enjoy

2.) the improper way, works equally well:
just reduce van der waals radius of zinc to zero
what you get is an unrestrained refinement of the
zinc position. Since Zinc scatters exceptionally well
this refinement works even at non-atomic resolution.

Best regards
Marius

> 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

PD Dr. habil. Marius Schmidt
Physikdepartment E17
Technische Universitaet Muenchen
James Franck Strasse
85747 Garching/Germany
email: marius.schmidt@ph.tum.de
http://users.physik.tu-muenchen.de/marius/

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CCP4bb <-- 2007 <-- April 2007 <-- 26 April 2007

Previous message:
Subject: Re: R and Rfree
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-26

Next message:
Subject: Error with scala after combat
From: Paola Llinas paola {- dot -} llinas {- at -} CURIE {- dot -} FR
Date: 2007-04-26