[phenixbb] ligand - protein close contact

Tanner, John J. TannerJJ at missouri.edu
Tue Jun 6 12:36:11 PDT 2017

I had a similar problem in Feb. 2017 with a sulfate ion running into a flavin. It turned out the PDB file mistakenly had a “LINK” line forcing a covalent bond where there should not have been one. I deleted the LINK line from the PDB file and everything was fine.

I think Pavel looked into the automatic linking algorithm with my files but I never heard of a resolution to the issue.

John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
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Email: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>
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On Jun 6, 2017, at 2:22 PM, Nikos Pinotsis <n.pinotsis at mail.cryst.bbk.ac.uk<mailto:n.pinotsis at mail.cryst.bbk.ac.uk>> wrote:

Dear all,

I have a protein-ligand structure with several chains in the AU. After refinement one of the ligands forms a close contact 1.8A with the protein. For the rest of the protein-ligand chains the same interaction is as expected to 2.7-2.8 A forming an H-bond. I tried to adjust this ligand with coot but everytime I am getting back the same 1.8 A close contact. There is enough density for the ligand and I can even see that it can fit better to distance 2.4-2.5A H-bond with the protein
Is there a way to constrain this distance to more than 2A? Should I fix the ligand atom that interacts? Unless I am missing something more fundamental. The ligand cif file is the default in phenix, the data set is a quite decent 2.3A.

thanks in advance for any suggestions

Dr. Nikos Pinotsis
Institute of Structural and Molecular Biology
Department of Biological Sciences, 3rd Floor, R313
Birkbeck College
Malet Street
London WC1E 7HX
T: +44 (0)207 631 6827
F: +44 (0)207 631 6803
M: +44 (0)792 384 3593

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