PMID: 2111014May 1, 1990Paper

Binding of substrate CO2 to the active site of human carbonic anhydrase II: a molecular dynamics study

Proceedings of the National Academy of Sciences of the United States of America
J Y Liang, W N Lipscomb

Abstract

Molecular dynamics has been used to study binding of substrate CO2 to the active site of human carbonic anhydrase II. Three potential CO2 binding sites have been located. The first is at the active-site hydrophobic pocket (the catalytically productive site), where CO2 is approximately 3.5 A from the zinc ion and interacts with His-94, His-119, Val-121, Val-143, Leu-198, Thr-199, the zinc ion, and the zinc-bound hydroxide ion. The second CO2 binding site is approximately 6 A from the zinc ion, where CO2 interacts with His-64, His-94, Leu-198, Thr-200, Pro-201, Pro-202, and some active-site water molecules. The third CO2 binding site is approximately 10 A from the zinc ion, is largely solvated by water molecules, and interacts with His-64, Asn-67, and Gln-92. At these three CO2 binding sites, the CO2 molecule is highly localized (the average Zn-CO2 distance fluctuation is approximately 1 A) and favors the linear binding orientation toward the zinc ion. This linear binding orientation of CO2 and its electrostatic interaction with the zinc ion direct diffusion of CO2 toward the zinc ion and facilitate the nucleophilic attack from O of the zinc-bound OH- to C of CO2 in the productive hydrophobic binding site. Finally, the two CO2 bi...Continue Reading

Citations

Jan 18, 2011·Journal of Computer-aided Molecular Design·Mattia FalconiAlessandro Desideri
Aug 1, 1991·Current Opinion in Biotechnology·J A TainerE D Getzoff
Jun 24, 2010·Journal of the American Chemical Society·Ruibo WuYingkai Zhang
Jun 13, 2009·Proceedings of the National Academy of Sciences of the United States of America·Björn SjöblomKristina Djinovic-Carugo
Sep 5, 2008·The Journal of Biological Chemistry·John F DomsicRobert McKenna
Jun 29, 2000·Annual Review of Biochemistry·D W Christianson, J D Cox
Mar 21, 2003·Biophysical Chemistry·Raja G Khalifah
Jan 1, 1997·Pharmacology & Therapeutics·S Lindskog
Aug 15, 2009·Biochimica Et Biophysica Acta·John F Domsic, Robert McKenna
Jul 3, 2015·The Journal of Physical Chemistry. B·Sanjib Paul, Srabani Taraphder
Nov 10, 2012·Journal of Enzyme Inhibition and Medicinal Chemistry·Mayank AggarwalRobert McKenna
Aug 2, 2011·Biochimica Et Biophysica Acta·Meghan E McDevitt, Lisa A Lambert
Apr 27, 2016·Proceedings of the National Academy of Sciences of the United States of America·Chae Un KimRobert McKenna
Nov 19, 1991·Biochemistry·R S AlexanderD W Christianson
Jan 28, 2003·Journal of Computational Chemistry·Jaroslav KocaRick L Ornstein
Jan 15, 1994·European Journal of Biochemistry·A LiljasY Xue
Jan 15, 2014·Organic & Biomolecular Chemistry·Xiang Sheng, Yongjun Liu
Nov 7, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Taremekedzwa Allan SanyangaÖzlem Tastan Bishop
Oct 12, 2018·International Journal of Medicinal Chemistry·Carrie L LomelinoRobert McKenna
Oct 22, 2016·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Elizabeth BrunkUrsula Rothlisberger
Feb 1, 1993·Proteins·M LindahlA Liljas
Jul 7, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Henrique S FernandesNuno M F S A Cerqueira
Jul 28, 2019·Free Radical Biology & Medicine·Yukako KomakiWilliam A Mitch
Dec 29, 2020·Journal of Biomolecular Structure & Dynamics·Pulala Raghuveer YadavPavan Kumar Pindi
Jul 2, 2021·Computational and Structural Biotechnology Journal·Vincenzo AlterioGiuseppina De Simone

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