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3i8d

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[[Image:3i8d.png|left|200px]]
 
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{{STRUCTURE_3i8d| PDB=3i8d | SCENE= }}
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==The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography==
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<StructureSection load='3i8d' size='340' side='right'caption='[[3i8d]], [[Resolution|resolution]] 1.61&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3i8d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I8D FirstGlance]. <br>
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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]] 1.61&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DFT:1-[2-DEOXYRIBOFURANOSYL]-2,4-DIFLUORO-5-METHYL-BENZENE-5MONOPHOSPHATE'>DFT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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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=3i8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i8d OCA], [https://pdbe.org/3i8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i8d RCSB], [https://www.ebi.ac.uk/pdbsum/3i8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i8d ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
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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/i8/3i8d_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=3i8d ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Certain DNA polymerases (pols) were found to efficiently insert A opposite the hydrophobic T isostere 2,4-difluorotoluene (F) and vice versa, resulting in the widely held belief that some pols rely on shape rather than H-bonding for accurate replication. Using X-ray crystallography we have analyzed the geometry of F:A pairs in duplex DNA and observed a distance between fluorine and the exocyclic amino group of A that is consistent with a H-bond, thus challenging the assumption that the F analogue is unable to engage in H-bonding as well as the steric hypothesis of DNA replication. Therefore, shape and H-bonding are inherently related, and steric constraints at a pol active site, or conferred by stacking or the DNA backbone conformation, may enable H-bonding by F.
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===The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography===
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Pairing Geometry of the Hydrophobic Thymine Analogue 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography.,Pallan PS, Egli M J Am Chem Soc. 2009 Aug 17. PMID:19685868<ref>PMID:19685868</ref>
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{{ABSTRACT_PUBMED_19685868}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 3i8d" style="background-color:#fffaf0;"></div>
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[[3i8d]] is a 4 chain structure of [[Ribonuclease]] with sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I8D OCA].
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==See Also==
==See Also==
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*[[Ribonuclease|Ribonuclease]]
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:019685868</ref><references group="xtra"/>
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__TOC__
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[[Category: Bacillus halodurans]]
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</StructureSection>
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[[Category: Ribonuclease H]]
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[[Category: Alkalihalobacillus halodurans]]
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[[Category: Egli, M.]]
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[[Category: Large Structures]]
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[[Category: Pallan, P S.]]
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[[Category: Egli M]]
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[[Category: 4-difluorotoluene]]
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[[Category: Pallan PS]]
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[[Category: Endonuclease]]
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[[Category: Hydrolase]]
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[[Category: Hydrolase-dna complex]]
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[[Category: Hydrophobic base]]
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[[Category: Magnesium]]
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[[Category: Manganese]]
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[[Category: Metal-binding]]
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[[Category: Nuclease]]
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[[Category: Rnase-h]]
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[[Category: Rnase-h dna-complex]]
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[[Category: Thymine isostere]]
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Current revision

The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography

PDB ID 3i8d

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