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==STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS==
==STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS==
<StructureSection load='1bna' size='340' side='right' caption='[[1bna]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='1bna' size='340' side='right'caption='[[1bna]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1bna]] is a 2 chain structure. The November 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_11 10.2210/rcsb_pdb/mom_2001_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BNA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BNA FirstGlance]. <br>
<table><tr><td colspan='2'>[[1bna]] is a 2 chain structure. The November 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_11 10.2210/rcsb_pdb/mom_2001_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BNA FirstGlance]. <br>
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=1bna RCSB], [http://www.ebi.ac.uk/pdbsum/1bna PDBsum]</span></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]] 1.9&#8491;</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=1bna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bna OCA], [https://pdbe.org/1bna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bna RCSB], [https://www.ebi.ac.uk/pdbsum/1bna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bna ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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<ref>PMID:6941276</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[DNA|DNA]]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
*[[Highest impact structures|Highest impact structures]]
*[[PDB identification code|PDB identification code]]
*[[Ribonuclease|Ribonuclease]]
*[[Temp|Temp]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA]]
[[Category: DNA]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Broka, C]]
[[Category: Broka C]]
[[Category: Dickerson, R E]]
[[Category: Dickerson RE]]
[[Category: Drew, H R]]
[[Category: Drew HR]]
[[Category: Itakura, K]]
[[Category: Itakura K]]
[[Category: Takano, T]]
[[Category: Takano T]]
[[Category: Tanaka, S]]
[[Category: Tanaka S]]
[[Category: Wing, R M]]
[[Category: Wing RM]]
[[Category: B-dna]]
[[Category: Dna]]
[[Category: Double helix]]

Latest revision as of 09:37, 7 February 2024

STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICSSTRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS

Structural highlights

1bna is a 2 chain structure. The November 2001 RCSB PDB Molecule of the Month feature on DNA by David S. Goodsell is 10.2210/rcsb_pdb/mom_2001_11. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

1bna, resolution 1.90Å

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