PMID: 8594192Feb 23, 1996Paper

Valence screening of water in protein crystals reveals potential Na+ binding sites

Journal of Molecular Biology
M Nayal, E Di Cera

Abstract

Identification of Na+ binding sites in protein crystals is complicated by comparable electron density of this monovalent cation and water. Valence calculations can predict the location of metal ion binding sites in proteins with high precision. These calculations were used to screen 332,242 water molecules in 2742 protein structures reported in the Protein Data Bank (PDB), searching for molecules with Na+/- specific valence values V(Na+) > or = 1.0 v.u., as expected for a bound Na ion. Thirty-three water molecules (<0.01% of the total) were found be have V(Na+) > or = 1.0 v.u. and to be located within 3.5 A from at least two protein oxygen atoms. These water molecules, with a high Na+ -specific valence, do not have valences specific for other cations, like Li+, K+, Mg2+ or Ca2+. They belong to nine different proteins (deoxyribonuclease I, enolase, hen egg-white lysozyme, human lysozyme, phospholipase A2, proteinase A, rubredoxin, thrombin and phage T4 lysozyme) and appear with similar coordination geometry, typically octahedral, in the same place in multiple crystal structure determinations of the same protein. In the case of thrombin, the water molecule singled out by valence calculations is, in fact, a bound Na ion as demonst...Continue Reading

Citations

Jul 19, 2003·News in Physiological Sciences : an International Journal of Physiology Produced Jointly by the International Union of Physiological Sciences and the American Physiological Society·R F Rakowski, S Sagar
Jul 15, 2004·The Journal of Biological Chemistry·Agustin O PinedaEnrico Di Cera
Nov 4, 2005·The Journal of Biological Chemistry·Enrico Di Cera
May 12, 2007·Acta Biochimica Et Biophysica Sinica·Hajime HiramatsuRyo Shimizu
Nov 4, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·David C Holley, Michael P Kavanaugh
Aug 1, 2012·Journal of Molecular Modeling·Alexandru LupanRadu Silaghi-Dumitrescu
Nov 6, 2013·Proceedings of the National Academy of Sciences of the United States of America·Donald D F LooErnest M Wright
Dec 20, 2014·The Journal of Biological Chemistry·Huijong Han, Petri Kursula
Jul 28, 2016·The Journal of Biological Chemistry·David W Gohara, Enrico Di Cera
May 3, 2018·Nucleic Acids Research·Nina M FischerDavid van der Spoel
May 21, 2004·The Journal of Biological Chemistry·Agustin O PinedaEnrico Di Cera
Apr 11, 2008·Journal of Biomolecular Structure & Dynamics·Carlos H T P SilvaOtavio H Thiemann
Oct 4, 2006·Physiological Reviews·Michael J Page, Enrico Di Cera
Jan 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Daniel J D JohnsonJames A Huntington
Mar 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sadhna RanaEnrico Di Cera
Sep 28, 2014·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Hugo D CorreiaTeresa Santos-Silva
Dec 4, 2014·Proceedings of the National Academy of Sciences of the United States of America·Fabrizio MarinelliJosé D Faraldo-Gómez
Mar 7, 2014·Acta Crystallographica. Section D, Biological Crystallography·Shigeki AraiRyota Kuroki
Jun 20, 2018·Proceedings of the National Academy of Sciences of the United States of America·Emel FiciciJosé D Faraldo-Gómez
Nov 25, 1998·Protein Science : a Publication of the Protein Society·J Wouters
Aug 4, 2004·Journal of Bioinformatics and Computational Biology·Liping Wei, Russ B Altman
Dec 4, 2002·Proceedings of the National Academy of Sciences of the United States of America·Haruo Ogawa, Chikashi Toyoshima
Jul 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Oscar JuárezBlanca Barquera
Feb 25, 2003·Annual Review of Biophysics and Biomolecular Structure·Juan A Subirana, Montserrat Soler-Lopez
Dec 12, 2012·Quarterly Reviews of Biophysics·Pengyu RenNathan A Baker
Apr 21, 2011·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Vadim RimsaWilliam N Hunter
Jul 31, 2007·The EMBO Journal·Thorsten OstendorpGünter Fritz
May 7, 2015·Acta Crystallographica. Section D, Biological Crystallography·Nader MorshedPaul D Adams
Oct 3, 2012·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·José M OteroMark J van Raaij
Oct 4, 2013·Nature·Ryuta KanaiChikashi Toyoshima

❮ Previous
Next ❯

Related Concepts

Related Feeds

Bacterial Cell Wall Structure (ASM)

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.

Bacterial Cell Wall Structure

Bacterial cell walls are made of peptidoglycan (also called murein), which is made from polysaccharide chains cross-linked by unusual peptides containing D-amino acids. Here is the latest research on bacterial cell wall structures.

Related Papers

Acta Crystallographica. Section D, Biological Crystallography
Jan OndrácekJuraj Sedlácek
Acta Crystallographica. Section D, Biological Crystallography
Marian NovotnyGerard J Kleywegt
Journal of Molecular Biology
C C BlakeP J Artymiuk
Hang tian yi xue yu yi xue gong cheng = Space medicine & medical engineering
J DongR Bi
© 2021 Meta ULC. All rights reserved