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| [[Image:1b6y.gif|left|200px]]
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| {{Structure
| | ==3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES== |
| |PDB= 1b6y |SIZE=350|CAPTION= <scene name='initialview01'>1b6y</scene>
| | <StructureSection load='1b6y' size='340' side='right'caption='[[1b6y]]' scene=''> |
| |SITE=
| | == Structural highlights == |
| |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=EDC:N3,N4-ETHENO-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>EDC</scene>
| | <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> |
| |ACTIVITY=
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| |GENE=
| | <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> |
| |DOMAIN=
| | <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> |
| |RELATEDENTRY=
| | </table> |
| |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>
| | __TOC__ |
| }}
| | </StructureSection> |
| | | [[Category: Large Structures]] |
| '''3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE ADENINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS, 2 STRUCTURES'''
| | [[Category: Cosman M]] |
| | | [[Category: Cullinan D]] |
| | | [[Category: De Los Santos C]] |
| ==Overview==
| | [[Category: Eisenberg M]] |
| 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.
| | [[Category: Grollman AP]] |
| | | [[Category: Korobka A]] |
| ==About this Structure==
| | [[Category: Patel DJ]] |
| 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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| ==Reference==
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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]] | |
| [[Category: Cosman, M.]] | |
| [[Category: Cullinan, D.]] | |
| [[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.]] | |
| [[Category: deoxyribonucleic acid]] | |
| [[Category: edc]] | |
| [[Category: ethenodc]] | |
| [[Category: exocyclic lesion]] | |
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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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