1bd1
From Proteopedia
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|PDB= 1bd1 |SIZE=350|CAPTION= <scene name='initialview01'>1bd1</scene>, resolution 1.600Å | |PDB= 1bd1 |SIZE=350|CAPTION= <scene name='initialview01'>1bd1</scene>, resolution 1.600Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=TEA:TRIETHYLAMMONIUM ION'>TEA</scene> | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=TEA:TRIETHYLAMMONIUM+ION'>TEA</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bd1 OCA], [http://www.ebi.ac.uk/pdbsum/1bd1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bd1 RCSB]</span> | ||
}} | }} | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Heinemann, U.]] | [[Category: Heinemann, U.]] | ||
| - | [[Category: TEA]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[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 18:58:25 2008'' |
Revision as of 15:58, 30 March 2008
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| , resolution 1.600Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA
Overview
The DNA decamer d(CCAGGCCTGG) has been studied by X-ray crystallography. At a nominal resolution of 1.6 A, the structure was refined to R = 16.9% using stereochemical restraints. The oligodeoxyribonucleotide forms a straight B-DNA double helix with crystallographic dyad symmetry and ten base-pairs per turn. In the crystal lattice, DNA fragments stack end-to-end along the c-axis to form continuous double helices. The overall helical structure and, notably, the groove dimensions of the decamer are more similar to standard, fiber diffraction-determined B-DNA than A-tract DNA. A unique stacking geometry is observed at the CA/TG base-pair step, where an increased rotation about the helix axis and a sliding motion of the base-pairs along their long axes leads to a superposition of the base rings with neighboring carbonyl and amino functions. Three-center (bifurcated) hydrogen bonds are possible at the CC/GG base-pair steps of the decamer. In their common sequence elements, d(CCAGGCCTGG) and the related G.A mismatch decamer d(CCAAGATTGG) show very similar three-dimensional structures, except that d(CCAGGCCTGG) appears to have a less regularly hydrated minor groove. The paucity of minor groove hydration in the center of the decamer may be a general feature of G/C-rich DNA and explain its relative instability in the B-form of DNA.
About this Structure
1BD1 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystallographic study of one turn of G/C-rich B-DNA., Heinemann U, Alings C, J Mol Biol. 1989 Nov 20;210(2):369-81. PMID:2600970
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