3i8d: Difference between revisions

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{{Seed}}
[[Image:3i8d.png|left|200px]]


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==The Pairing Geometry of the Hydrophobic Thymine Analog 2,4-Difluorotoluene in Duplex DNA as Analyzed by X-ray Crystallography==
The line below this paragraph, containing "STRUCTURE_3i8d", creates the "Structure Box" on the page.
<StructureSection load='3i8d' size='340' side='right'caption='[[3i8d]], [[Resolution|resolution]] 1.61&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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>
{{STRUCTURE_3i8d|  PDB=3i8d  |  SCENE=  }}
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i8/3i8d_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


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


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3i8d" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_19685868}}, adds the Publication Abstract to the page
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 19685868 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_19685868}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Alkalihalobacillus halodurans]]
3I8D is a 4 chains structure of sequences 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].
[[Category: Large Structures]]
 
[[Category: Egli M]]
==Reference==
[[Category: Pallan PS]]
<ref group="xtra">PMID:19685868</ref><references group="xtra"/>
[[Category: Bacillus halodurans]]
[[Category: Ribonuclease H]]
[[Category: Egli, M.]]
[[Category: Pallan, P S.]]
[[Category: 4-difluorotoluene]]
[[Category: Cytoplasm]]
[[Category: Endonuclease]]
[[Category: Hydrolase]]
[[Category: Hydrolase/dna complex]]
[[Category: Hydrophobic base]]
[[Category: Magnesium]]
[[Category: Manganese]]
[[Category: Metal-binding]]
[[Category: Nuclease]]
[[Category: Rnase-h]]
[[Category: Rnase-h dna-complex]]
[[Category: Thymine isostere]]
[[Category: X-ray crystallography]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 16 08:32:43 2009''
Retrieved from "https://proteopedia.org/3i8d"