1d75: Difference between revisions
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|PDB= 1d75 |SIZE=350|CAPTION= <scene name='initialview01'>1d75</scene>, resolution 2.800Å | |PDB= 1d75 |SIZE=350|CAPTION= <scene name='initialview01'>1d75</scene>, resolution 2.800Å | ||
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= <scene name='pdbligand=A38:8-OXY+DEOXYADENOSINE-5'-MONOPHOSPHATE'>A38</scene>, <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> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d75 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d75 OCA], [http://www.ebi.ac.uk/pdbsum/1d75 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d75 RCSB]</span> | |||
}} | }} | ||
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[[Category: modified]] | [[Category: modified]] | ||
''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 19:35:56 2008'' | ||
Revision as of 19:36, 30 March 2008
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| , resolution 2.800Å | |||||||
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CONFORMATION OF THE GUANINE.8-OXOADENINE BASE PAIRS IN THE CRYSTAL STRUCTURE OF D(CGCGAATT(O8A)GCG)
OverviewOverview
The structure of the synthetic deoxydodecamer d(CGCGAATT(O8A)GCG)2 (O8A = 8-oxoadenine) has been determined by single-crystal X-ray diffraction techniques. The oligonucleotide crystallizes in the orthorhombic space group P2(1)2(1)2(1) with cell dimensions of a = 25.48 A, b = 41.84 A, and c = 64.91 A. The refinement has converged with an R-factor of 0.151 for 1119 reflections in the resolution range 8.0-2.25 A. Sixty-seven solvent molecules were located during the course of the refinement. The B-DNA helix consists of ten Watson-Crick base pairs and two guanine-8-oxoadenine (G.O8A) base pairs. In order to achieve hydrogen-bonding complementarity between the two bases, an unusual G(anti).O8A-(syn) wobble conformation is adopted. It is proposed that the G.O8A mispairs are held together by a network of four interbase hydrogen bonds which are the result of the formation of two reverse three-center hydrogen-bonding systems. These involve one carbonyl oxygen lone pair interacting with two hydrogen atoms. In a departure from previous observations of the characteristics of purine-purine anti-syn base pairs, lambda 1 and lambda 2, the angles between the glycosidic bonds and the C1'-C1' vector, are symmetric. A reassessment of the other purine-purine mispairs suggests that similar three-center hydrogen bonds may occur and make a contribution to stabilizing other base pairings.
About this StructureAbout this Structure
1D75 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Conformation of guanine-8-oxoadenine base pairs in the crystal structure of d(CGCGAATT(O8A)GCG)., Leonard GA, Guy A, Brown T, Teoule R, Hunter WN, Biochemistry. 1992 Sep 15;31(36):8415-20. PMID:1390625
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