399d

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|PDB= 399d |SIZE=350|CAPTION= <scene name='initialview01'>399d</scene>, resolution 1.9&Aring;
|PDB= 399d |SIZE=350|CAPTION= <scene name='initialview01'>399d</scene>, resolution 1.9&Aring;
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|LIGAND= <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=399d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=399d OCA], [http://www.ebi.ac.uk/pdbsum/399d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=399d RCSB]</span>
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[[Category: double helix]]
[[Category: double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:55:21 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:22:10 2008''

Revision as of 02:22, 31 March 2008

Image:399d.gif


PDB ID 399d

Drag the structure with the mouse to rotate
, resolution 1.9Å
Ligands: ,
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



STRUCTURE OF D(CGCCCGCGGGCG)


Overview

We have determined the structure of the dodecamer duplex d(CGCCCGCGGGCG)2. A careful use of the molecular replacement programme AMoRe has been essential in order to solve the structure. This dodecamer shows a unique conformation, quite different from all the previously studied oligonucleotide duplexes: the central octamer has an A conformation, but with a sharp 65 degrees kink in the centre; the terminal base-steps have a B-like conformation; the major groove is completely closed in the centre, a hollow molecule is thus found. The results obtained confirm the high degree of variability of DNA structure. A new type of kink and an intermediate A/B double-helical conformation have been found. Such intermediate conformation differs from those described in DNA polymerase complexes.

About this Structure

399D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

Structure of the d(CGCCCGCGGGCG) dodecamer: a kinked A-DNA molecule showing some B-DNA features., Malinina L, Fernandez LG, Huynh-Dinh T, Subirana JA, J Mol Biol. 1999 Jan 29;285(4):1679-90. PMID:9917405

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