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1bna

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|PDB= 1bna |SIZE=350|CAPTION= <scene name='initialview01'>1bna</scene>, resolution 1.900&Aring;
|PDB= 1bna |SIZE=350|CAPTION= <scene name='initialview01'>1bna</scene>, resolution 1.900&Aring;
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bna OCA], [http://www.ebi.ac.uk/pdbsum/1bna PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bna 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 10:13:17 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:04:24 2008''

Revision as of 16:04, 30 March 2008

Image:1bna.jpg


PDB ID 1bna

Drag the structure with the mouse to rotate
, resolution 1.900Å
Ligands: , , ,
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS


Overview

The crystal structure of the synthetic DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error of R = 17.8% at 1.9-A resolution (two-sigma data). The molecule forms slightly more than one complete turn of right-handed double-stranded B helix. The two ends of the helix overlap and interlock minor grooves with neighboring molecules up and down a 2(1) screw axis, producing a 19 degrees bend in helix axis over the 11-base-pair steps of the dodecamer. In the center of the molecule, where perturbation is least, the helix has a mean rotation of 36.9 degrees per step, or 9.8 base pairs per turn. The mean propeller twist (total dihedral angle between base planes) between A . T base pairs in the center of the molecule is 17.3 degrees, and that between C . G pairs on the two ends averages 11.5 degrees. Individual deoxyribose ring conformations as measured by the C5'-C4'-C3'-O3' torsion angle delta, exhibit an approximately Gaussian distribution centered around the C1'-exo position with delta avg = 123 degrees and a range of 79 degrees to 157 degrees. Purine sugars cluster at high delta values, and pyrimidine sugars cluster at lower delta. A tendency toward 2-fold symmetry in sugar conformation about the center of the molecule is detectable in spite of the destruction of ideal 2-fold symmetry by the molecular bending. More strikingly, sugar conformations of paired based appear to follow a "principle of anticorrelation," with delta values lying approximately the same distance to either side of the center value, delta = 123 degrees. This same anticorrelation is also observed in other DNA and DNA . RNA structures.

About this Structure

1BNA is a Protein complex structure of sequences from [1]. The following page contains interesting information on the relation of 1BNA with [DNA]. Full crystallographic information is available from OCA.

Reference

Structure of a B-DNA dodecamer: conformation and dynamics., Drew HR, Wing RM, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE, Proc Natl Acad Sci U S A. 1981 Apr;78(4):2179-83. PMID:6941276

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