1bna: Difference between revisions
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'''STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS''' | '''STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS''' | ||
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==About this Structure== | ==About this Structure== | ||
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== | ||
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:[http://www.ncbi.nlm.nih.gov/pubmed/6941276 6941276] | 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:[http://www.ncbi.nlm.nih.gov/pubmed/6941276 6941276] | ||
[[Category: DNA]] | [[Category: DNA]] | ||
[[Category: Broka, C.]] | [[Category: Broka, C.]] | ||
[[Category: Dickerson, R E.]] | [[Category: Dickerson, R E.]] | ||
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[[Category: Tanaka, S.]] | [[Category: Tanaka, S.]] | ||
[[Category: Wing, R M.]] | [[Category: Wing, R M.]] | ||
[[Category: | [[Category: B-dna]] | ||
[[Category: | [[Category: Double helix]] | ||
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Revision as of 11:43, 2 May 2008
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
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 Page seeded by OCA on Fri May 2 11:43:38 2008