214d
From Proteopedia
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|PDB= 214d |SIZE=350|CAPTION= <scene name='initialview01'>214d</scene> | |PDB= 214d |SIZE=350|CAPTION= <scene name='initialview01'>214d</scene> | ||
|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=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=T41:1-(2-O-METHYL-BETA-D-ARABINOFURANOSYL)THYMIDINE+5'-MONOPHOSPHATE'>T41</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=214d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=214d OCA], [http://www.ebi.ac.uk/pdbsum/214d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=214d RCSB]</span> | ||
}} | }} | ||
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[[Category: nmr]] | [[Category: nmr]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:44:17 2008'' |
Revision as of 22:44, 30 March 2008
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
THE SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING A SINGLE 2'-O-METHYL-BETA-D-ARAT
Overview
Two-dimensional 1H NMR spectroscopy was used to determine the solution structure of the double-stranded DNA oligonucleotide d(5'-CGCATATAGCC-3'): d(5'-GGCTAXATGCG-3'), where X is 1-(2-O-methyl-beta-D-arabinofuranosyl)thymine. The structure determination was based on a total relaxation matrix analysis of NOESY cross-peak intensities using the MARDIGRAS program. The improved RANDMARDI procedure was used during the calculations to include the experimental "noise" in the NOESY spectra. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the modified DNA duplex from both A-form and B-form DNA starting structures. The root-mean-square deviation of the coordinates for the 40 structures was 0.82 A. The duplex adopts a normal B-DNA-type helix, and the spectra as well as the structure show that the modified nucleotide X adopts a C2'-endo (S) sugar conformation. There are no significant changes in the helix originating from the modified nucleotide. The CH3O group on X is directed toward the major groove, and there seems to be free space for further modifications at this position.
About this Structure
214D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of a DNA duplex containing a single 2'-O-methyl-beta-D-araT: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement., Gotfredsen CH, Spielmann HP, Wengel J, Jacobsen JP, Bioconjug Chem. 1996 Nov-Dec;7(6):680-8. PMID:8950487
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