[phenixbb] NAG-ASN link geometry

nihmayerm mayerm at mail.nih.gov
Thu Oct 23 14:57:55 PDT 2008

We are refining a 2.7 A structure with multiple ASN-NAG links using  
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,  
including those refined with PHENIX.

The NAG-ASN link used by PHENIX 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 - MLM

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