1f6j: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1f6j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F6J FirstGlance]. <br>
<table><tr><td colspan='2'>[[1f6j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F6J FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1f69|1f69]], [[1f6c|1f6c]], [[1f6e|1f6e]], [[1f6i|1f6i]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</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=1f6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6j OCA], [https://pdbe.org/1f6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f6j RCSB], [https://www.ebi.ac.uk/pdbsum/1f6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6j ProSAT]</span></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=1f6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f6j OCA], [https://pdbe.org/1f6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f6j RCSB], [https://www.ebi.ac.uk/pdbsum/1f6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f6j ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cytosine methylation or bromination of the DNA sequence d(GGCGCC)2 is shown here to induce a novel extended and eccentric double helix, which we call E-DNA. Like B-DNA, E-DNA has a long helical rise and bases perpendicular to the helix axis. However, the 3'-endo sugar conformation gives the characteristic deep major groove and shallow minor groove of A-DNA. Also, if allowed to crystallize for a period of time longer than that yielding E-DNA, the methylated sequence forms standard A-DNA, suggesting that E-DNA is a kinetically trapped intermediate in the transition to A-DNA. Thus, the structures presented here chart a crystallographic pathway from B-DNA to A-DNA through the E-DNA intermediate in a single sequence. The E-DNA surface is highly accessible to solvent, with waters in the major groove sitting on exposed faces of the stacked nucleotides. We suggest that the geometry of the waters and the stacked base pairs would promote the spontaneous deamination of 5-methylcytosine in the transition mutation of dm5C-dG to dT-dA base pairs.
The extended and eccentric E-DNA structure induced by cytosine methylation or bromination.,Vargason JM, Eichman BF, Ho PS Nat Struct Biol. 2000 Sep;7(9):758-61. PMID:10966645<ref>PMID:10966645</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1f6j" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Eichman, B F]]
[[Category: Eichman BF]]
[[Category: Ho, P S]]
[[Category: Ho PS]]
[[Category: Vargason, J M]]
[[Category: Vargason JM]]
[[Category: Dna]]
[[Category: Double helix]]
[[Category: E-dna]]
[[Category: Methylation]]

Latest revision as of 10:11, 7 February 2024

CRYSTAL STRUCTURE OF THE E-DNA HEXAMER GGCGBR5CCCRYSTAL STRUCTURE OF THE E-DNA HEXAMER GGCGBR5CC

Structural highlights

1f6j is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.25Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1f6j, resolution 2.25Å

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