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 <lynn.gregory-pau...@ipbs.fr>
*To:* CCP4BB@JISCMAIL.AC.UK
*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:
markus.rudo...@bio.uni-goettingen.de
<mailto:markus.rudo...@bio.uni-goettingen.de>
> 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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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
lynn.gregory-pau...@ipbs.fr <mailto:lynn.gregory-pau...@ipbs.fr>\par
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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
lynn.gregory-pau...@ipbs.fr\par
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