1b5k: Difference between revisions

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-[[Image:1b5k.png|left|200px]]
-<!--
+==3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE THYMIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS==
-The line below this paragraph, containing "STRUCTURE_1b5k", creates the "Structure Box" on the page.
+<StructureSection load='1b5k' size='340' side='right'caption='[[1b5k]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1b5k]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B5K FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
--->
+<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>
-{{STRUCTURE_1b5k|  PDB=1b5k  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b5k OCA], [https://pdbe.org/1b5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b5k RCSB], [https://www.ebi.ac.uk/pdbsum/1b5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b5k ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The exocyclic 3,N4-etheno-2'-deoxycytidine adduct was incorporated at the center of the oligodeoxynucleotide duplex d(C-G-T-A-C-epsilon C-C-A-T-G-C).d (G-C-A-T-G-T-G-T-A-C-G), and its solution structure was analyzed using high-resolution proton NMR spectroscopy and molecular dynamics simulations. The experimental data indicate that the oligodeoxynucleotide duplex adopts a right-handed helical structure with sugar puckers in the C2'-endo/C3'-exo range and Watson-Crick hydrogen bond alignments for all base pairs. NOE connectivities established a syn orientation for the glycosidic torsion angle of the exocyclic adduct. Restrained molecular dynamics simulations, using the full relaxation matrix approach, produced a three-dimensional model in agreement with the experimental data. The structure shows only minor perturbations in the sugar-phosphate backbone and a 27 degrees bend of the helical axis at the lesion site. On the refined model a well-formed hydrogen bond between T (N3H) and epsilon C(N4) stabilizes the epsilon C(syn).T(anti) base pair alignment, reflecting the preference of the adduct for the syn orientation. Furthermore, the epsilon C(syn).T(anti) base pair stacks with flanking base pairs. We discuss a correlation between the mutagenic properties of the adduct and the three-dimensional structure of the epsilon C.dA and epsilon C.T duplexes.
-===3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE THYMIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS===
+NMR solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite thymidine: comparison with the duplex containing deoxyadenosine opposite the adduct.,Cullinan D, Korobka A, Grollman AP, Patel DJ, Eisenberg M, de los Santos C Biochemistry. 1996 Oct 15;35(41):13319-27. PMID:8873598<ref>PMID:8873598</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_8873598}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1b5k" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 8873598 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_8873598}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[1b5k]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B5K OCA].
+[[Category: Cullinan D]]
+[[Category: De Santos CL]]
-==Reference==
+[[Category: Eisenberg M]]
-<ref group="xtra">PMID:008873598</ref><ref group="xtra">PMID:010677286</ref><references group="xtra"/>
+[[Category: Grollman AP]]
-[[Category: Cullinan, D.]]
+[[Category: Korobka A]]
-[[Category: Eisenberg, M.]]
+[[Category: Patel DJ]]
-[[Category: Grollman, A P.]]
-[[Category: Korobka, A.]]
-[[Category: Patel, D J.]]
-[[Category: Santos, C De L.]]
-[[Category: Dna]]
-[[Category: Edc]]
-[[Category: Ethenodc]]
-[[Category: Exocyclic lesion]]