Hi Jan,
at low occupancy (and I suppose a resolution that does not extend beyond 2.0 A),
you have to rely on your restraints. I think the consensus is that the adenine
ring
should be planar. The pyridine ring of the nicotinamide should be flat if the
ring
is oxidized (NAD+), and can be distorted when reduced (NADH).
Most NAD molecules in the PDB have strict planar restaints in the pyridine ring
of the nicotinamide, even when the density clearly shows that they are puckered.
Many NAD+ cofactors get converted to NADH during crystallization by the enzyme
they bind. Especially PEG can contain a substrates to convert NAD+ into NADH
in the crystal.
Best regards,
Rob Meijers
Synchrotron Soleil
--- On Thu, 3/19/09, Jan Abendroth <jan.abendr...@gmail.com> wrote:
From: Jan Abendroth <jan.abendr...@gmail.com>
Subject: [ccp4bb] nad woes
To: CCP4BB@JISCMAIL.AC.UK
Date: Thursday, March 19, 2009, 12:50 AM
Hi all,
is there any wisdom on NAD out there? I experience some strange behaviour of
this common cofactor.
With moderately convincing density, probably low occupancy of a cofactor that
came along for the ride from E coli, Refmac5.5.0088 pulls the AN6 atom out of
the adenine plane. With my own library that puts planar restraints on the
adenine ring this seems to be fixed.
Coot during real space refinement or regularisation using either the standard
or my own dictionary handles the purine ring just fine, however, totally garbles
up the nicotineamide.
Btw, I use the * nomenclature.
Cheers
Jan
--
Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island WA, USA
work: JAbendroth_at_decode.is
home: Jan.Abendroth_at_gmail.com
