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| - | [[Image:1jo2.gif|left|200px]] | |
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| - | {{Structure
| + | ==Crystal Structure of the B-DNA Hexamer (CgATCG).Daunomycin Complex Containing a Ribose at the Intercalation Site== |
| - | |PDB= 1jo2 |SIZE=350|CAPTION= <scene name='initialview01'>1jo2</scene>, resolution 1.50Å
| + | <StructureSection load='1jo2' size='340' side='right'caption='[[1jo2]], [[Resolution|resolution]] 1.50Å' 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=DM1:DAUNOMYCIN'>DM1</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>
| + | <table><tr><td colspan='2'>[[1jo2]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JO2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JO2 FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DM1:DAUNOMYCIN'>DM1</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=1jo2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jo2 OCA], [https://pdbe.org/1jo2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jo2 RCSB], [https://www.ebi.ac.uk/pdbsum/1jo2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jo2 ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jo2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jo2 OCA], [http://www.ebi.ac.uk/pdbsum/1jo2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jo2 RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''Crystal Structure of the B-DNA Hexamer (CgATCG).Daunomycin Complex Containing a Ribose at the Intercalation Site'''
| + | [[Category: Pan B]] |
| - | | + | [[Category: Shi K]] |
| - | | + | [[Category: Sundaralingam M]] |
| - | ==Overview==
| + | |
| - | The crystal structure of a DNA/RNA chimera (dC)(rG)d(ATCG) complexed with the anticancer drug daunomycin has been determined at 1.5 A resolution with R(work) and R(free) of 19.7 and 23.3%, respectively, for 2767 reflections. The complex crystallizes in space group P4(1)2(1)2, with unit-cell parameters a = b = 28.05, c = 53.16 A, and contains one nucleic acid strand and one daunomycin molecule in the asymmetric unit. To our knowledge, this is the first crystal structure of a DNA/RNA chimera complexed with an intercalating drug. The DNA/RNA chimera adopts the B-form helical conformation, with the 2'-hydroxyl group in the major groove of the duplex, forming hydrogen bonds to N7 and the anionic phosphate oxygen of its 3'-side adenine. The present results indicate that the replacement by the ribose sugar in the DNA sequence does not change the geometry and intercalation pattern of daunomycin. A model of B-form RNA has been built based on the present structure. The model indicates that the interactions of the 2'-hydroxyl groups in the B-form duplex depend on their 3'-side nucleotides.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1JO2 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=1JO2 OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 A resolution., Shi K, Pan B, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1377-83. Epub 2003, Jul 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12876339 12876339]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Pan, B.]] | + | |
| - | [[Category: Shi, K.]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: dna/rna chimer]]
| + | |
| - | [[Category: intercalation]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:36:24 2008''
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