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Re: [ccp4bb]: Again:CO2-conformation
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I highly doubt that what you are seeing is a linear CO2 molecule. Carbon
dioxide has no net charge and no net dipole moment, making it more
hydrophobic. As of last year, no linear CO2 molecules have been observed in
the PDB. When listed, they are typically carbamylated lysine residues...see
Rubisco and phosphotriesterase structures for examples. If you think that you
have a CO2 in your structure, the most likely place would be in a hydrophobic
pocket...not next to an arginine. Many enzymologists even argue that even when
CO2 is a substrate in a reaction, one can argue that it does not have a bona
fide binding site and that its is mearly a bimolecular collision. So, unless
you have added CO2 to your mother liquor, perhaps under pressure, then you are
probably seeing some sort of anomaly. To suggest CO2 at this point is very
arguable without any evidence of direct binding measurements.
Andy Mesecar
At 07:16 PM 10/22/2002 +0200, Juergen J. Mueller wrote:
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>
>Dear all,
>to clarify:
>Our molecule (electron density) is linear, it should be CO2. It is
>trapped in front of an ARG.
>In the Refmac5 dictionary exist only an entry for a kinked CO2 (
>CO2 O1 C O2 109.470 3.000).
>May be, there is a problem with the nomenclature and that should not be
>carbon dioxide?
>Greetings,
>Juergen
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Andrew D. Mesecar
Assistant Professor
Department of Medicinal Chemistry and Pharmacognosy
and the Center for Pharmaceutical Biotechnology
(MC 870) MBRB Room 3070
900 South Ashland Avenue
Chicago, IL 60607
Ear-Mail 312-996-1877 (office)
E-mail mesecar@uic.edu
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