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1b6y

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[[Image:1b6y.gif|left|200px]]
 
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{{Structure
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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==
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|PDB= 1b6y |SIZE=350|CAPTION= <scene name='initialview01'>1b6y</scene>
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<StructureSection load='1b6y' size='340' side='right'caption='[[1b6y]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[1b6y]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B6Y FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDC:N3,N4-ETHENO-2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>EDC</scene></td></tr>
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}}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b6y OCA], [https://pdbe.org/1b6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b6y RCSB], [https://www.ebi.ac.uk/pdbsum/1b6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b6y ProSAT]</span></td></tr>
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</table>
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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'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Cosman M]]
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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.
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[[Category: Cullinan D]]
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[[Category: De Los Santos C]]
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==About this Structure==
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[[Category: Eisenberg M]]
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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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[[Category: Grollman AP]]
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[[Category: Korobka A]]
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==Reference==
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[[Category: Patel DJ]]
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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]]
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[[Category: Cosman, M.]]
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[[Category: Cullinan, D.]]
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[[Category: Eisenberg, M.]]
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[[Category: Grollman, A P.]]
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[[Category: Korobka, A.]]
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[[Category: Patel, D J.]]
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[[Category: Santos, C De Los.]]
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[[Category: deoxyribonucleic acid]]
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[[Category: edc]]
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[[Category: ethenodc]]
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[[Category: exocyclic lesion]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:07:07 2008''
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Current revision

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

PDB ID 1b6y

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