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1snc

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[[Image:1snc.gif|left|200px]]
 
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{{Structure
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==THE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF STAPHYLOCOCCAL NUCLEASE, CA2+, AND THE INHIBITOR PD*TP, REFINED AT 1.65 ANGSTROMS==
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|PDB= 1snc |SIZE=350|CAPTION= <scene name='initialview01'>1snc</scene>, resolution 1.65&Aring;
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<StructureSection load='1snc' size='340' side='right'caption='[[1snc]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=THP:THYMIDINE-3&#39;,5&#39;-DIPHOSPHATE'>THP</scene>
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<table><tr><td colspan='2'>[[1snc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SNC FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.31.1 3.1.31.1]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1snc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1snc OCA], [https://pdbe.org/1snc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1snc RCSB], [https://www.ebi.ac.uk/pdbsum/1snc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1snc ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NUC_STAAU NUC_STAAU] Enzyme that catalyzes the hydrolysis of both DNA and RNA at the 5' position of the phosphodiester bond.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sn/1snc_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1snc ConSurf].
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<div style="clear:both"></div>
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'''THE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF STAPHYLOCOCCAL NUCLEASE, CA2+, AND THE INHIBITOR PD*TP, REFINED AT 1.65 ANGSTROMS'''
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==See Also==
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*[[Staphylococcal nuclease|Staphylococcal nuclease]]
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__TOC__
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==Overview==
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</StructureSection>
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The structure of a complex of staphylococcal nuclease with Ca2+ and deoxythymidine 3',5'-bisphosphate (pdTp) has been refined by stereochemically restrained least-squares minimization to a crystallographic R value of 0.161 at 1.65 A resolution. The estimated root-mean-square (rms) error in the coordinates is 0.16 A. The final model comprises 1082 protein atoms, one calcium ion, the pdTp molecule, and 82 solvent water molecules; it displays an rms deviation from ideality of 0.017 A for bond distances and 1.8 degrees for bond angles. The mean distance between corresponding alpha carbons in the refined and unrefined structures is 0.6 A; we observe small but significant differences between the refined and unrefined models in the turn between residues 27 and 30, the loop between residues 44 and 50, the first helix, and the extended strand between residues 112 and 117 which forms part of the active site binding pocket. The details of the calcium liganding and solvent structure in the active site are clearly shown in the final electron density map. The structure of the catalytic site is consistent with the mechanism that has been proposed for this enzyme. However, we note that two lysines from a symmetry-related molecule in the crystal lattice may play an important role in determining the geometry of inhibitor binding, and that only one of the two required calcium ions is observed in the crystal structure; thus, caution is advised in extrapolating from the structure of the complex of enzyme and inhibitor to that of enzyme and substrate.
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[[Category: Large Structures]]
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==About this Structure==
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1SNC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SNC OCA].
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==Reference==
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The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A., Loll PJ, Lattman EE, Proteins. 1989;5(3):183-201. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2780539 2780539]
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[[Category: Micrococcal nuclease]]
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[[Category: Single protein]]
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[[Category: Staphylococcus aureus]]
[[Category: Staphylococcus aureus]]
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[[Category: Lattman, E E.]]
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[[Category: Lattman EE]]
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[[Category: Loll, P J.]]
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[[Category: Loll PJ]]
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[[Category: CA]]
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[[Category: THP]]
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[[Category: hydrolase (phosphoric diester)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 13:38:01 2008''
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Current revision

THE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF STAPHYLOCOCCAL NUCLEASE, CA2+, AND THE INHIBITOR PD*TP, REFINED AT 1.65 ANGSTROMS

PDB ID 1snc

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