Re: [ccp4bb] Distinguish NH4 from Na?
Dear Jacob, You may find useful this web site by Marjorie Harding about metal coordination sites in proteins http://tanna.bch.ed.ac.uk/ best regards Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ Bio-organic Chemistry Laboratory Faculty of Science and Technology Free University of Bolzano Piazza Università, 5 39100 Bolzano, Italy Office (room K2.14): +39 0471 017128 Laboratory (room E.012): +39 0471 017901 Fax: +39 0471 017009 *** -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, 16 November, 2011 19:21 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Distinguish NH4 from Na? Dear Crystallographers, I have crystals containing 666mM NH4 and 540mM Na, and there appears to be a water which is only about 2.2 Ang from some polar atoms. It is currently reasonably happy as a Na, but is there any reasonable way to decide which cation is there? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Distinguish NH4 from Na?
Dear Jacob, for NH4+, you would expect a (partial) tetrahedral coordination with typical H-bond distances of ~2.9 A. For Na+, you would expect a (partial) octahedral coordination with Metal-to-ligand distances of ~2.4 A (see Harding, Acta Cryst., D62, 678-682 (2006); Harding, Acta Cryst., D58, 872-874 (2002); Glusker, Advances in Protein Chemistry, 42, 1-76 (1991)). But depending on your data resolution and quality, and on the completeness of the coordination sphere, it might be difficult to distinguish between them. Best regards, Dirk. Am 16.11.11 19:20, schrieb Jacob Keller: Dear Crystallographers, I have crystals containing 666mM NH4 and 540mM Na, and there appears to be a water which is only about 2.2 Ang from some polar atoms. It is currently reasonably happy as a Na, but is there any reasonable way to decide which cation is there? JPK -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] Distinguish NH4 from Na?
Dear Crystallographers, I have crystals containing 666mM NH4 and 540mM Na, and there appears to be a water which is only about 2.2 Ang from some polar atoms. It is currently reasonably happy as a Na, but is there any reasonable way to decide which cation is there? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Distinguish NH4 from Na?
Bond valence sum Muller et al. Acta Cryst. (2003). D59, 32-37 if the resolution is good (better than 1.8 A) R On 16 Nov 2011, at 18:20, Jacob Keller wrote: Dear Crystallographers, I have crystals containing 666mM NH4 and 540mM Na, and there appears to be a water which is only about 2.2 Ang from some polar atoms. It is currently reasonably happy as a Na, but is there any reasonable way to decide which cation is there? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.uk
Re: [ccp4bb] Distinguish NH4 from Na?
Dear JPK, I think the coordination geometry of Na is a key, normally it adopts octahedral geometry with Na---O distances of 2.1-2.2 ang, whereas water molecule is h-bonded with H-acceptor or H-donor with the distances between 2.6-3.3 ang. I am not sure it is correct, as i used to be small-molecule X-ray worker. stephen Quoting Steiner, Roberto roberto.stei...@kcl.ac.uk: Bond valence sum Muller et al. Acta Cryst. (2003). D59, 32-37 if the resolution is good (better than 1.8 A) R On 16 Nov 2011, at 18:20, Jacob Keller wrote: Dear Crystallographers, I have crystals containing 666mM NH4 and 540mM Na, and there appears to be a water which is only about 2.2 Ang from some polar atoms. It is currently reasonably happy as a Na, but is there any reasonable way to decide which cation is there? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** Roberto Steiner, PhD Randall Division of Cell and Molecular Biophysics Group Leader King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.uk -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
