1bna: Difference between revisions
New page: left|200px<br /> <applet load="1bna" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bna, resolution 1.900Å" /> '''STRUCTURE OF A B-D... |
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'''STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS'''<br /> | '''STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS'''<br /> | ||
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==About this Structure== | ==About this Structure== | ||
1BNA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. The following page contains interesting information on the relation of 1BNA with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb23_1.html DNA]]. Full crystallographic information is available from [http:// | 1BNA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. The following page contains interesting information on the relation of 1BNA with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb23_1.html DNA]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BNA OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: double helix]] | [[Category: double helix]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 15:32:43 2008'' | ||
Revision as of 16:32, 15 February 2008
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STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS
OverviewOverview
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 StructureAbout 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.
ReferenceReference
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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