4ygk: Difference between revisions

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-'''Unreleased structure'''
-The entry 4ygk is ON HOLD
+==NaSCN--Interactions between Hofmeister Anions and the Binding Pocket of a Protein==
+<StructureSection load='4ygk' size='340' side='right'caption='[[4ygk]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ygk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YGK FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=SCN:THIOCYANATE+ION'>SCN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ygk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ygk OCA], [https://pdbe.org/4ygk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ygk RCSB], [https://www.ebi.ac.uk/pdbsum/4ygk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ygk ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[https://omim.org/entry/259730 259730]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+This paper uses the binding pocket of human carbonic anhydrase II (HCAII, EC 4.2.1.1) as a tool to examine the properties of Hofmeister anions that determine (i) where, and how strongly, they associate with concavities on the surfaces of proteins and (ii) how, upon binding, they alter the structure of water within those concavities. Results from X-ray crystallography and isothermal titration calorimetry show that most anions associate with the binding pocket of HCAII by forming inner-sphere ion pairs with the Zn(2+) cofactor. In these ion pairs, the free energy of anion-Zn(2+) association is inversely proportional to the free energetic cost of anion dehydration; this relationship is consistent with the mechanism of ion pair formation suggested by the "law of matching water affinities". Iodide and bromide anions also associate with a hydrophobic declivity in the wall of the binding pocket. Molecular dynamics simulations suggest that anions, upon associating with Zn(2+), trigger rearrangements of water that extend up to 8 A away from their surfaces. These findings expand the range of interactions previously thought to occur between ions and proteins by suggesting that (i) weakly hydrated anions can bind complementarily shaped hydrophobic declivities, and that (ii) ion-induced rearrangements of water within protein concavities can (in contrast with similar rearrangements in bulk water) extend well beyond the first hydration shells of the ions that trigger them. This study paints a picture of Hofmeister anions as a set of structurally varied ligands that differ in size, shape, and affinity for water and, thus, in their ability to bind to-and to alter the charge and hydration structure of-polar, nonpolar, and topographically complex concavities on the surfaces of proteins.
-Authors: Jerome M. Fox, Kyungtae Kang, Woody Sherman, Annie Heroux, Madhavi Sestry, Mostafa Baghbanzadeh, Matthew R. Lockett, and George M. Whitesides
+Interactions between Hofmeister Anions and the Binding Pocket of a Protein.,Fox JM, Kang K, Sherman W, Heroux A, Sastry GM, Baghbanzadeh M, Lockett MR, Whitesides GM J Am Chem Soc. 2015 Mar 25;137(11):3859-66. doi: 10.1021/jacs.5b00187. Epub 2015 , Mar 17. PMID:25738615<ref>PMID:25738615</ref>
-Description: NaSCN--Interactions between Hofmeister Anions and the Binding Pocket of a Protein
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Jerome M. Fox, Kyungtae Kang, Woody Sherman, Annie Heroux, Madhavi Sestry, Mostafa Baghbanzadeh, Matthew R. Lockett, And George M. Whitesides]]
+<div class="pdbe-citations 4ygk" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Carbonic anhydrase 3D structures|Carbonic anhydrase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Baghbanzadeh M]]
+[[Category: Fox JM]]
+[[Category: Heroux A]]
+[[Category: Kang K]]
+[[Category: Lockett MR]]
+[[Category: Sastry GM]]
+[[Category: Sherman W]]
+[[Category: Whitesides GM]]