No, there's no cacocylate in the drop, but thanks for the suggestion.
Lynn
MARTYN SYMMONS a écrit :
> Dear Lynn - you don't have cacodylate around do you? - there is a DTT
> catalyzed modification of Cys by that (several examples in the pdb) -
> just a thought.
> regards
> Martyn
>
> ------------------------------------------------------------------------
> *From:* Lynn Gregory-Pauron <[log in to unmask]>
> *To:* [log in to unmask]
> *Sent:* Tuesday, 23 June, 2009 9:11:28 AM
> *Subject:* Re: [ccp4bb] Solvent-exposed Cys and an unidentified ligand
>
> Thank you for your reply. I don't actually see anything interacting
> with what would be the second SH of the DTT. The atom opposite the Cys
> sulfur is at a distance of 3.0 A (could this eventually suggest
> hydrogen bonding)?? I have been looking at examples in the PDB, and
> have found a few protein structures where the first S of an extended
> DTT is 3.0 A away from the S of Cys. Is this feasible for 2 sulfurs
> to be 3.0 A apart, and can I apply this to my structure?
> Lynn
>
> Markus Rudolph a écrit :
> > Lynn,
> >
> > if DTT is connected via its sulfur to Cys (2.03A distance), it is
> oxidized and the DTT is extended.
> >
> > The interesting question then is: why do you see such a
> constellation since the cyclic oxidized DTT is more stable than the
> linear with a nearby thiol group? could the second SH in DTT be
> involved in another interaction?
> >
> > HTH,
> >
> > Markus
> >
> >
> >
> >
> ___________________________________________________________________________________
> >
> > Markus Rudolph phone: +41 61 68-86420
> > Dept. Mol. Struct. Biol.
> > Georg-August University e-mail:
> [log in to unmask]
> <mailto:[log in to unmask]>
> > Justus-von-Liebig-Weg 11
> www.img.bio.uni-goettingen.de/ms-www/index.html
> <http://www.img.bio.uni-goettingen.de/ms-www/index.html>
> > 37077 Goettingen, Germany
> www.gpmolbio.uni-goettingen.de/faculty/f_rudolph.html
> <http://www.gpmolbio.uni-goettingen.de/faculty/f_rudolph.html>
> >
> ___________________________________________________________________________________
> >
> >
> > On Mon, 22 Jun 2009, Lynn Gregory-Pauron wrote:
> >
> >
> >> My structure has a Cys that is solvent-exposed and an unidentified
> 'blob' of
> >> density which is connected to the sulfur of the Cys. The protein was
> >> crystallized in presence of DTT, and DTT does fit the density.
> However, I do
> >> not know if it is oxidized or not, as the density does not appear to
> >> accommodate the ring conformation of oxidized DTT. Does anyone
> know of an
> >> article that talks about the chemistry of DTT, reducing agents in
> >> crystallographic structures or have any suggestions as to what is
> going on?
> >> Thank you,
> >> Lynn
> >>
> >>
> >>
>
>
> --
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> {\*\generator Msftedit 5.41.15.1515;}\viewkind4\uc1\pard\f0\fs24 Lynn
> Gregory-Pauron\par
> Institut de Pharmacologie et de Biologie Structurale (IPBS)\par
> CNRS \endash Universit\'e9 de Toulouse\par
> 205 route de Narbonne\par
> Toulouse, 31077\par
> France\par
> T\'e9l. + 33 (0) 5 61 17 54 40 \par
> [log in to unmask] <mailto:[log in to unmask]>\par
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> }
--
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{\*\generator Msftedit 5.41.15.1515;}\viewkind4\uc1\pard\f0\fs24 Lynn Gregory-Pauron\par
Institut de Pharmacologie et de Biologie Structurale (IPBS)\par
CNRS \endash Universit\'e9 de Toulouse\par
205 route de Narbonne\par
Toulouse, 31077\par
France\par
T\'e9l. + 33 (0) 5 61 17 54 40 \par
[log in to unmask]\par
\f1\fs20\par
}
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