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1stg

From Proteopedia

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[[Image:1stg.jpg|left|200px]]
 
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{{Structure
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==TWO DISTINCTLY DIFFERENT METAL BINDING MODES ARE SEEN IN X-RAY CRYSTAL STRUCTURES OF STAPHYLOCOCCAL NUCLEASE-COBALT(II)-NUCLEOTIDE COMPLEXES==
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|PDB= 1stg |SIZE=350|CAPTION= <scene name='initialview01'>1stg</scene>, resolution 1.70&Aring;
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<StructureSection load='1stg' size='340' side='right'caption='[[1stg]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=THP:THYMIDINE-3&#39;,5&#39;-DIPHOSPHATE'>THP</scene>
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<table><tr><td colspan='2'>[[1stg]] 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=1STG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1STG FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[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] </span>
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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]] 1.7&#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=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=THP:THYMIDINE-3,5-DIPHOSPHATE'>THP</scene></td></tr>
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|DOMAIN=
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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=1stg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1stg OCA], [https://pdbe.org/1stg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1stg RCSB], [https://www.ebi.ac.uk/pdbsum/1stg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1stg ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1stg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1stg OCA], [http://www.ebi.ac.uk/pdbsum/1stg PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1stg RCSB]</span>
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== Function ==
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}}
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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/st/1stg_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=1stg ConSurf].
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<div style="clear:both"></div>
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'''TWO DISTINCTLY DIFFERENT METAL BINDING MODES ARE SEEN IN X-RAY CRYSTAL STRUCTURES OF STAPHYLOCOCCAL NUCLEASE-COBALT(II)-NUCLEOTIDE COMPLEXES'''
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==See Also==
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*[[Staphylococcal nuclease 3D structures|Staphylococcal nuclease 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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Two crystal structures of ternary complexes of staphylococcal nuclease, cobalt(II), and the mononucleotide pdTp are reported. The first has been refined at 1.7 A to a crystallographic R value of 0.198; the second, determined from a crystal soaked for 9 months in a slightly different mother liquor than the first crystal, has been refined at 1.85 A to an R value of 0.174. In the first structure, the cobalt ion is displaced 1.94 A from the normal calcium position, and the active site is dominated by a salt bridge between Asp-21 and Lys-70 from a symmetry-related molecule in the crystal lattice. The Co2+ ion appears unable to displace this lysine; consequently, the metal is bound in a vestibular site adjacent to the calcium site. The metal-binding pocket in the second structure adopts a configuration similar to that of the calcium complex, with the cobalt ion binding only 0.36 A from the calcium position. However, an inner sphere water seen in the calcium structure is missing from this structure. The cobalt ion in the second structure appears to be loosely or transiently coordinated within the calcium binding pocket, as evidenced by the high value of its refined thermal factor. Loss of catalytic activity for cobalt(II)-substituted nuclease is perhaps due to its inability to bind this inner sphere water.
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[[Category: Large Structures]]
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==About this Structure==
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1STG 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=1STG OCA].
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==Reference==
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X-ray crystal structures of staphylococcal nuclease complexed with the competitive inhibitor cobalt(II) and nucleotide., Loll PJ, Quirk S, Lattman EE, Garavito RM, Biochemistry. 1995 Apr 4;34(13):4316-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7703245 7703245]
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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: Quirk, S.]]
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[[Category: Quirk S]]
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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 30 23:46:44 2008''
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Current revision

TWO DISTINCTLY DIFFERENT METAL BINDING MODES ARE SEEN IN X-RAY CRYSTAL STRUCTURES OF STAPHYLOCOCCAL NUCLEASE-COBALT(II)-NUCLEOTIDE COMPLEXES

PDB ID 1stg

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