114d: Difference between revisions
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|PDB= 114d |SIZE=350|CAPTION= <scene name='initialview01'>114d</scene>, resolution 2.500Å | |PDB= 114d |SIZE=350|CAPTION= <scene name='initialview01'>114d</scene>, resolution 2.500Å | ||
|SITE= | |SITE= | ||
|LIGAND= | |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=DI:2'-DEOXYINOSINE-5'-MONOPHOSPHATE'>DI</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=114d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=114d OCA], [http://www.ebi.ac.uk/pdbsum/114d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=114d 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 18:26:51 2008'' | ||
Revision as of 18:26, 30 March 2008
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| , resolution 2.500Å | |||||||
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
INOSINE-ADENINE BASE PAIRS IN A B-DNA DUPLEX
OverviewOverview
The structure of the synthetic deoxydodecamer d(C-G-C-I-A-A-T-T-A-G-C-G) has been determined by single crystal X-ray diffraction techniques at 2.5A resolution. The refinement converged with a crystallographic residual, R = 0.19 and the location of 64 solvent molecules. The sequence crystallises as a B-DNA helix with 10 Watson-Crick base-pairs (4 A.T. and 6 G.C) and 2 inosine.adenine (I.A) pairs. The present work shows that in the purine.purine base-pairs the adenine adopts syn orientation with respect to the furanose moiety while the inosine is in the trans (anti) orientation. Two hydrogen bonds link the I.A. base-pair, one between N-1(I) and N-7(A), the other between O-6(I) and N-6(A). This bulky purine.purine base-pair is incorporated in the double helix at two positions with little distortion of either local or global conformation. The pairing observed in this study is presented as a model for I.A base-pairs in RNA codon-anticodon interactions and may help explain the thermodynamic stability of inosine containing base-pairs. Conformational parameters and base stacking interactions are presented and where appropriate compared with those of the native compound, d(C-G-C-G-A-A-T-T-C-G-C-G) and with other studies of oligonucleotides containing purine.purine base-pairs.
About this StructureAbout this Structure
114D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Inosine.adenine base pairs in a B-DNA duplex., Corfield PW, Hunter WN, Brown T, Robinson P, Kennard O, Nucleic Acids Res. 1987 Oct 12;15(19):7935-49. PMID:3671069
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