We are refining a 2.7 A structure with multiple ASN-NAG links. The torsion angle between the Asn amide and the sugar is quite variable, while from the chemistry of this link we would expect a value close to 180°, as reported in the PDB survey by Imberty & Perez (Protein Engineering 8:669-709).
A quick look at some entries in the PDB revealed close to textbook geometry for the NAG- ASN link in structures around 1Å resolution (e.g. 1UWC) and gets much worse in some lower resolution structures. We are using PHENIX for this refinement, but the same problem occures with Rremac, because the two programs use the same monomer library. The NAG-ASN link does not contain a torsion angle definition, and I would like to ask (i) if its appropriate to use one in refinement, and if so (2) could people share their cif file for this link. Thanks
