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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.
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<div class="">I think Pavel looked into the automatic linking algorithm with my files but I never heard of a resolution to the issue. </div>
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John J. Tanner<br class="">
Professor of Biochemistry and Chemistry</div>
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Department of Biochemistry</div>
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University of Missouri-Columbia<br class="">
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Lab: Schlundt Annex rooms 3,6,9, 203B, 203C</div>
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<div class="">On Jun 6, 2017, at 2:22 PM, Nikos Pinotsis <<a href="mailto:n.pinotsis@mail.cryst.bbk.ac.uk" class="">n.pinotsis@mail.cryst.bbk.ac.uk</a>> wrote:</div>
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<div class="">Dear all,<br class="">
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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<br class="">
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.<br class="">
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thanks in advance for any suggestions<br class="">
Nikos<br class="">
<br class="">
-- <br class="">
Dr. Nikos Pinotsis<br class="">
Institute of Structural and Molecular Biology<br class="">
Department of Biological Sciences, 3rd Floor, R313<br class="">
Birkbeck College<br class="">
Malet Street<br class="">
London WC1E 7HX<br class="">
T: +44 (0)207 631 6827<br class="">
F: +44 (0)207 631 6803<br class="">
M: +44 (0)792 384 3593<br class="">
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