1f6c

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[[Image:1f6c.gif|left|200px]]<br /><applet load="1f6c" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1f6c.gif|left|200px]]
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caption="1f6c, resolution 2.7&Aring;" />
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'''CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE'''<br />
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{{Structure
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|PDB= 1f6c |SIZE=350|CAPTION= <scene name='initialview01'>1f6c</scene>, resolution 2.7&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>
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|ACTIVITY=
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|GENE=
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}}
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'''CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1F6C is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=SPM:'>SPM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F6C OCA].
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1F6C is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F6C OCA].
==Reference==
==Reference==
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10966645 10966645]
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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: Protein complex]]
[[Category: Protein complex]]
[[Category: Eichman, B F.]]
[[Category: Eichman, B F.]]
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[[Category: e-dna]]
[[Category: e-dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:35:19 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:05:01 2008''

Revision as of 09:05, 20 March 2008

Image:1f6c.gif


PDB ID 1f6c

Drag the structure with the mouse to rotate
, resolution 2.7Å
Ligands:
Coordinates: save as pdb, mmCIF, xml



CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE


Overview

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.

About this Structure

1F6C is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

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

Page seeded by OCA on Thu Mar 20 11:05:01 2008

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