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| [[Image:1a9i.gif|left|200px]]
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| {{Structure
| | ==APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, ALPHA FORM, NMR, 1 STRUCTURE== |
| |PDB= 1a9i |SIZE=350|CAPTION= <scene name='initialview01'>1a9i</scene>
| | <StructureSection load='1a9i' size='340' side='right'caption='[[1a9i]]' scene=''> |
| |SITE=
| | == Structural highlights == |
| |LIGAND= <scene name='pdbligand=AAB:2-DEOXY-5-PHOSPHORIBOSE+GROUP'>AAB</scene>, <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>
| | <table><tr><td colspan='2'>[[1a9i]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A9I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A9I 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=AAB:2-DEOXY-RIBOFURANOSE-5-MONOPHOSPHATE'>AAB</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=1a9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a9i OCA], [https://pdbe.org/1a9i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a9i RCSB], [https://www.ebi.ac.uk/pdbsum/1a9i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a9i ProSAT]</span></td></tr> |
| |RELATEDENTRY=
| | </table> |
| |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1a9i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a9i OCA], [http://www.ebi.ac.uk/pdbsum/1a9i PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1a9i RCSB]</span>
| | __TOC__ |
| }}
| | </StructureSection> |
| | | [[Category: Large Structures]] |
| '''APYRIMIDINIC DNA WITH BOUND WATER AT THE DAMAGED SITE, ALPHA FORM, NMR, 1 STRUCTURE'''
| | [[Category: Beger RD]] |
| | | [[Category: Bolton PH]] |
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| ==Overview==
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| Natural and exogenous processes can give rise to abasic sites with either a purine or pyrimidine as the base on the opposing strand. The solution state structures of the apyrimidinic DNA duplex, with D6 indicating an abasic site, [sequence: see text] referred to as AD, and the apurinic DNA duplex with a dC17, referred to as CD, have been determined. A particularly striking difference is that the abasic site in CD is predominantly a beta hemiacetal, whereas in AD the alpha and beta forms are equally present. Hydrogen bonding with water by the abasic site and the base on the opposite strand appears to play a large role in determining the structure near the damaged site. Comparison of these structures with that of a duplex DNA containing a thymine glycol at the same position as the abasic site and with that of a duplex DNA containing an abasic site in the middle of a curved DNA sequence offers some insight into the common and distinct structural features of damaged DNA sites.
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| ==About this Structure==
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| 1A9I 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=1A9I OCA].
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| ==Reference==
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| Structures of apurinic and apyrimidinic sites in duplex DNAs., Beger RD, Bolton PH, J Biol Chem. 1998 Jun 19;273(25):15565-73. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9624147 9624147]
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| [[Category: Protein complex]] | |
| [[Category: Beger, R D.]] | |
| [[Category: Bolton, P H.]] | |
| [[Category: apyrimidinic dna]]
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| [[Category: damaged dna]]
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| [[Category: water]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:36:11 2008''
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