Re: [ccp4bb] Unidentified ligand (electron density) found at active site

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CCP4bb <-- 2007 <-- December 2007 <-- 06 December 2007

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Subject: Re: Unidentified ligand (electron density) found at active site
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2007-12-06

Hi,

Why is it that you are so reluctant to identify this compound
as Ser-Gly? Its fit to the density is great.

To wax historical, we saw unexpected density in the active site
of "apo" Thermolysin. It appeared to be Val-Ala, but with refinement
it developed into Val-Lys. It happens that Val-Lys are the last
two residues of the protein. Residues 315 and 316 were present at
full occupancy in the crystal so I presume the peptide was clipped
off molecules that didn't crystallize.

Of course proving that the density actually represents Ser-Gly,
or any other compound you decide upon is much harder than building
a model to fit the density. What is harder than identifying a bit
of density, is coming up with an experiment to prove it.

Dale Tronrud

Ronaldo Alves Pinto Nagem wrote:
> Dear CCP4bb users,
>
> As suggested by some users, I am attaching to this email the electron
> density of the unidentified ligand. As I mentioned before it looks like a
> dipeptide GlySer, but we are still in doubt. Attempts to correlate with
> the protein function are being done. One might see in the pictures that
> the ligand coordinate a metal ion.
>
> Cheers
>
> Ronaldo.
>
>
>
> ---------------------------------------------------------
> Prof. Dr. Ronaldo Alves Pinto Nagem
> Universidade Federal de Minas Gerais
> Instituto de Ciências Biológicas
> Departamento de Bioquímica e Imunologia
> Av. Antônio Carlos, 6627 - Caixa Postal 486
> Bairro Pampulha - CEP: 31270-901
> Belo Horizonte, MG - Brasil
> Tel: +55 31 3499-2626
> Fax: +55 31 3499-2614
> E-mail: nagem@icb.ufmg.br
>
>
> ------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------
>

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CCP4bb <-- 2007 <-- December 2007 <-- 06 December 2007

Previous message:
Subject: The BNL-Biology and NSLS Course on Synchrotron Data Collection: Please Apply
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From: Engin Ozkan eozkan {- at -} STANFORD {- dot -} EDU
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