[ccp4bb] NAD dihedral for C2N-C3N-C7N-N7N

[Jorge Iulek]

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 close to either 0 or 180 degrees, but in most cases it is to one of these, with a preference towards 0 degrees. Another search in the literature, and I could not find any study on either NAD or even the nicotinamide alone to calculate the energy barrier to rotate around this bond (in vacuum, eg).     My data quality and resolution do not put much confidence on B-factor differences, but they seem to indicate that the cited dihedral angle should be close to 180 degrees, id est, O7N is "closer" to C2N (and, consequently, to N1N) than N7N is. In fact, I have a glutamine nearby whose terminal amide is interacting with the nicotinamide amide, so my idea is to make one's nitrogen to interact with other's oxygen. Concerning b-factor differences for this glutamine, they favor its NE2 to point to nicotinamide amide, what would imply that the C2N-C3N-C7N-N7N dihedral to would be close to 180 degrees rather than 0 degree.     Is there any wide study on NAD nicotinamide amide conformation? Specially, bound to protein structures?     Thanks, Jorge