[phenixbb] [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine

David Briggs david.briggs at crick.ac.uk
Mon Jun 21 23:11:35 PDT 2021

Hi Jiang Xu,

(Phenixbb added as I suspect this is Phenix not coot that has caused your issue)

Did you check the "add hydrogens" button in Phenix.refine? Sometimes this can erroneously add a second H to the ND of glycosylated Asn residues. (I assume this is because bond distances in the input PDB file fall outside Phenix's definitions of an Asn-NAG link).

If the second H is added, this breaks the refinement of the Asn-NAG bond.

My work around is to run "Ready Set" to add hydrogens as a separate job, and then manually inspect and correct the Asn residues as necessary before running Phenix.refine and _not_ checking the "add hydrogens" box.

I hope this fixes your problem.

Good luck,


Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK

From: CCP4 bulletin board <CCP4BB at JISCMAIL.AC.UK> on behalf of Jiang Xu <foxjuly at GMAIL.COM>
Sent: Tuesday, June 22, 2021 6:47:36 AM
Subject: [ccp4bb] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine

External Sender: Use caution.

Hello guys,
   I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a dashed line, rather than a solid line in Coot. After refinement of the structure using Phenix.refine, I found the bond just disappeared, and the amine group still has two hydrogen atoms, which should contain one hydrogen atom.  So,  how to solve this problem?
Thank you,
Jiang Xu
Lin Chen's Research Group
University of Southern California


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