100d: Difference between revisions
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|PDB= 100d |SIZE=350|CAPTION= <scene name='initialview01'>100d</scene>, resolution 1.900Å | |PDB= 100d |SIZE=350|CAPTION= <scene name='initialview01'>100d</scene>, resolution 1.900Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=SPM:SPERMINE'>SPM</scene> | |LIGAND= <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=100d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=100d OCA], [http://www.ebi.ac.uk/pdbsum/100d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=100d RCSB]</span> | |||
}} | }} | ||
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[[Category: Ramakrishnan, B.]] | [[Category: Ramakrishnan, B.]] | ||
[[Category: Sundaralingam, M.]] | [[Category: Sundaralingam, M.]] | ||
[[Category: a-dna/rna]] | [[Category: a-dna/rna]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:26:18 2008'' | ||
Revision as of 18:26, 30 March 2008
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| , resolution 1.900Å | |||||||
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING
OverviewOverview
The crystal structure of the self-complementary chimeric decamer duplex r(C)d(CGGCGCCG)r(G), with RNA base pairs at both termini, has been solved at 1.9 A resolution by the molecular replacement method and refined to an R value of 0.145 for 2,314 reflections. The C3'-endo sugar puckers of the terminal riboses apparently drive the entire chimeric duplex into an A-DNA conformation, in contrast to the B-DNA conformation adopted by the all-deoxy decamer of the same sequence. Five symmetry related duplexes encapsulate a spermine molecule which interacts with ten phosphate groups, both directly and through water molecules to form multiple ionic and hydrogen bonding interactions. The spermine interaction severely bends the duplexes by 31 degrees into the major groove at the fourth base pair G(4).C(17), jolts it and slides the 'base plate' into the minor groove. This base pair, together with the adjacent base pair in the top half and the corresponding pseudo two-fold related base pairs in the bottom half, form four minor groove base-paired multiples with the terminal base pairs of two neighboring duplexes.
About this StructureAbout this Structure
100D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing., Ban C, Ramakrishnan B, Sundaralingam M, Nucleic Acids Res. 1994 Dec 11;22(24):5466-76. PMID:7816639
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