1f69: Difference between revisions

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{{Seed}}
[[Image:1f69.png|left|200px]]


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==CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE==
The line below this paragraph, containing "STRUCTURE_1f69", creates the "Structure Box" on the page.
<StructureSection load='1f69' size='340' side='right'caption='[[1f69]], [[Resolution|resolution]] 2.60&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'>[[1f69]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F69 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F69 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]] 2.6&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
{{STRUCTURE_1f69|  PDB=1f69  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f69 OCA], [https://pdbe.org/1f69 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f69 RCSB], [https://www.ebi.ac.uk/pdbsum/1f69 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f69 ProSAT]</span></td></tr>
</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.


===CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE===
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>
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<div class="pdbe-citations 1f69" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 10966645 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_10966645}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F69 OCA].
[[Category: Eichman BF]]
 
[[Category: Ho PS]]
==Reference==
[[Category: Vargason JM]]
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:[http://www.ncbi.nlm.nih.gov/pubmed/10966645 10966645]
[[Category: Eichman, B F.]]
[[Category: Ho, P S.]]
[[Category: Vargason, J M.]]
[[Category: B-dna]]
[[Category: Double helix]]
[[Category: E-dna]]
 
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