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1d26
From Proteopedia
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|PDB= 1d26 |SIZE=350|CAPTION= <scene name='initialview01'>1d26</scene>, resolution 2.120Å | |PDB= 1d26 |SIZE=350|CAPTION= <scene name='initialview01'>1d26</scene>, resolution 2.120Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=G31:3'-METHYL-2',3'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE'>G31</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d26 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d26 OCA], [http://www.ebi.ac.uk/pdbsum/1d26 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d26 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 19:33:05 2008'' |
Revision as of 16:33, 30 March 2008
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| , resolution 2.120Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
EFFECT OF A SINGLE 3'-METHYLENE PHOSPHONATE LINKAGE ON THE CONFORMATION OF AN A-DNA OCTAMER DOUBLE HELIX
Overview
The three-dimensional structure of the self-complementary DNA octamer d(GCCCGpGGC) has been determined in the crystalline state using X-ray diffraction data to a nominal resolutoin of 2.12 measured from a very small crystal at DESY, Hamburg. The structure was refined with stereochemical restraints to an R value of 17.1%. d(GCCCGpGGC), containing one single 3'-methylene phosphonate linkage (denoted p), forms an A-DNA double helix with strict dyad symmetry, that is distinct from canonical A-DNA by a wide open major groove and a small average base-pair inclination against the helix axis. The conformation of the unmodified control d(GCCCGGGC) is known from an X-ray analysis of isomorphous crystals (Heinemann et al. (1987) Nucleic Acids Res. 15, 9531-9550). Comparison of the two structures reveals only minor conformational differences, most notably in the pucker of the reduced deoxyribose. It is suggested that oligonucleotides with charged 3'-methylene phosphonate groups may form stable duplexes with complementary DNA or RNA strands rendering them candidates for use as gene-regulatory antisense probes.
About this Structure
1D26 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Effect of a single 3'-methylene phosphonate linkage on the conformation of an A-DNA octamer double helix., Heinemann U, Rudolph LN, Alings C, Morr M, Heikens W, Frank R, Blocker H, Nucleic Acids Res. 1991 Feb 11;19(3):427-33. PMID:2011517
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