1b6y

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[[Image:1b6y.gif|left|200px]]
[[Image:1b6y.gif|left|200px]]
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{{Structure
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|PDB= 1b6y |SIZE=350|CAPTION= <scene name='initialview01'>1b6y</scene>
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The line below this paragraph, containing "STRUCTURE_1b6y", creates the "Structure Box" on the page.
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|SITE=
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=EDC:N3,N4-ETHENO-2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>EDC</scene>
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{{STRUCTURE_1b6y| PDB=1b6y | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6y OCA], [http://www.ebi.ac.uk/pdbsum/1b6y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1b6y RCSB]</span>
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'''3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES'''
'''3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES'''
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==About this Structure==
==About this Structure==
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1B6Y is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6Y OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6Y OCA].
==Reference==
==Reference==
Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics., Korobka A, Cullinan D, Cosman M, Grollman AP, Patel DJ, Eisenberg M, de los Santos C, Biochemistry. 1996 Oct 15;35(41):13310-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8873597 8873597]
Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics., Korobka A, Cullinan D, Cosman M, Grollman AP, Patel DJ, Eisenberg M, de los Santos C, Biochemistry. 1996 Oct 15;35(41):13310-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8873597 8873597]
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[[Category: Protein complex]]
 
[[Category: Cosman, M.]]
[[Category: Cosman, M.]]
[[Category: Cullinan, D.]]
[[Category: Cullinan, D.]]
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[[Category: Patel, D J.]]
[[Category: Patel, D J.]]
[[Category: Santos, C De Los.]]
[[Category: Santos, C De Los.]]
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[[Category: deoxyribonucleic acid]]
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[[Category: Deoxyribonucleic acid]]
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[[Category: edc]]
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[[Category: Edc]]
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[[Category: ethenodc]]
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[[Category: Ethenodc]]
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[[Category: exocyclic lesion]]
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[[Category: Exocyclic lesion]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 11:08:55 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:54:56 2008''
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Revision as of 08:08, 2 May 2008

Image:1b6y.gif

Template:STRUCTURE 1b6y

3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES


Overview

The d(C-G-T-A-C-epsilon C-C-A-T-G-C).d(G-C-A-T-G-A-G-T-A-C-G) oligodeoxynucleotide duplex containing the 3, N4-etheno-2'-deoxycytidine adduct positioned opposite 2'-deoxyadenosine in the center of the helix has been analyzed by proton NMR spectroscopy and restrained molecular dynamics. The spectroscopic data establish a right-handed duplex, with sugar puckers in the C2'-endo/C3'-exo range, residues adopting an anti conformation around the glycosidic torsion angle and, with the exception of epsilon C.dA, Watson-Crick hydrogen bond alignment for all base pairs. Molecular dynamics simulations, restrained by the full relaxation matrix approach, produced a three-dimensional model with an NMR R-factor of 7%. The duplex structure shows no significant perturbation of the sugar-phosphate backbone, which remains in B-form. The exocyclic adduct and its partner dA are incorporated into the helix without producing a noticeable kink. The epsilon C.dA alignment adopts a staggered conformation with each residue displaced toward the 5'-terminus and intercalated between bases on the opposite strand, without increase of inter-phosphate distances. The partial intercalation of the epsilon C (anti).dA(anti) alignment allows stacking between the aromatic rings of epsilon C and dA and with base pairs adjacent to the lesion, suggesting an important role played by hydrophobic forces in the stabilization of the solution structure.

About this Structure

Full crystallographic information is available from OCA.

Reference

Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2'-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics., Korobka A, Cullinan D, Cosman M, Grollman AP, Patel DJ, Eisenberg M, de los Santos C, Biochemistry. 1996 Oct 15;35(41):13310-8. PMID:8873597 Page seeded by OCA on Fri May 2 11:08:55 2008

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