1iey
From Proteopedia
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|PDB= 1iey |SIZE=350|CAPTION= <scene name='initialview01'>1iey</scene> | |PDB= 1iey |SIZE=350|CAPTION= <scene name='initialview01'>1iey</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=OCT:N-OCTANE'>OCT</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=OCT:N-OCTANE'>OCT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1iek|1IEK]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iey OCA], [http://www.ebi.ac.uk/pdbsum/1iey PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1iey RCSB]</span> | ||
}} | }} | ||
| Line 29: | Line 32: | ||
[[Category: Orozco, M.]] | [[Category: Orozco, M.]] | ||
[[Category: Soliva, R.]] | [[Category: Soliva, R.]] | ||
| - | [[Category: OCT]] | ||
[[Category: charge neutralization]] | [[Category: charge neutralization]] | ||
[[Category: dna bending]] | [[Category: dna bending]] | ||
| Line 35: | Line 37: | ||
[[Category: modified oligonucleotide]] | [[Category: modified oligonucleotide]] | ||
| - | ''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 21:18:51 2008'' |
Revision as of 18:18, 30 March 2008
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| Ligands: | , , , , | ||||||
| Related: | 1IEK
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SOLUTION STRUCTURE OF THE DNA DUPLEX D(CCACCGGAAC).(GTTCCGGTGG) WITH A CHIRAL ALKYL-PHOSPHONATE MOIETY (DIAESTEREOISOMER R)
Overview
The solution structures of two DNA decamers of sequence d(CCACCpxGGAAC).(GTTCCGGTGG) with a chiral alkyl phosphonate moiety (px) have been determined using NMR and restrained molecular dynamics simulations and compared with the solution structure of the unmodified duplex. The (1)H NMR spectra of two samples with pure stereochemistry in the modified phosphate have been assigned. The structures of both diastereoisomers, as well as the unmodified control duplex, have been determined from NMR-derived distance and torsion angle constraints. Accurate distance constraints were obtained from a complete relaxation matrix analysis of the NOE intensities. The structures have been refined with state of the art molecular dynamics methods, including explicit solvent and applying the particle mesh Ewald method to properly evaluate the long-range electrostatic interactions. In both cases, the calculations converge to well-defined structures, with RMSDs of approximately 1 A. The resulting structures belong to the general B family of DNA structures, even though the presence of the alkyl phosphonate moiety induces some slight displacement to the A-form in the neighborhood of the modified phosphate. Partial neutralization of this phosphate and the steric effect of the alkyl moiety provoke moderate bending in the DNA. This effect is more pronounced in the S diastereoisomer, where the alkyl group points inwards to the double helix.
About this Structure
1IEY is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety., Soliva R, Monaco V, Gomez-Pinto I, Meeuwenoord NJ, Marel GA, Boom JH, Gonzalez C, Orozco M, Nucleic Acids Res. 2001 Jul 15;29(14):2973-85. PMID:11452022
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