Thanks
Victor, Dale and John for inputs concerning this question. Yes,
always to check the cif files. I will look carefully at the
hydrogen bond network, though both conformations might be
possible; right now I am testing both and I will check better
There are theories that the NAD carboxamide group in an enzyme active
site should be out of the nicotine plane by 20-30 degrees, to help
develop a partial positive charge on the C4 atom. This also helps
distorting the planarity of the nicotine ring to ease the catalytic
transformation of NAD to
I have looked over a number of high resolution models with NAD+ and
NADH in the PDB as well as small molecule structures. I also have some
familiarity with similar chemistry in the decorations on the edge of
bacteriochlorophyll-a molecules. The CONH2 group does flip over when
the hydrogen bond
I’m not aware of a wide study on NAD carboxamide conformation. Lacking atomic
resolution, optimizing the hydrogen bonding can be used to determine the
orientation of the carboxamide, as you wrote. You may have to consider
intramolecular hydrogen bonding within NAD+ as well as intermolecular hydr
Dear all,
I came across some difficulty to refine a NAD molecule in a
structure, specially its amide of the nicotinamide moiety.
A (very) brief search in deposited structures seems to point
that not so ever the C2N-C3N-C7N-N7N dihedral is
