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1em0

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[[Image:1em0.gif|left|200px]]
 
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{{Structure
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==COMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN==
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|PDB= 1em0 |SIZE=350|CAPTION= <scene name='initialview01'>1em0</scene>, resolution 0.9&Aring;
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<StructureSection load='1em0' size='340' side='right'caption='[[1em0]], [[Resolution|resolution]] 0.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CBR:5-BROMO-2&#39;-DEOXY-CYTIDINE-5&#39;-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PNI:TETRA[N-METHYL-PYRIDYL]+PORPHYRIN-NICKEL'>PNI</scene>
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<table><tr><td colspan='2'>[[1em0]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EM0 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">X-ray diffraction, [[Resolution|Resolution]] 0.9&#8491;</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=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PNI:TETRA[N-METHYL-PYRIDYL]+PORPHYRIN-NICKEL'>PNI</scene></td></tr>
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|DOMAIN=
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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=1em0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1em0 OCA], [https://pdbe.org/1em0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1em0 RCSB], [https://www.ebi.ac.uk/pdbsum/1em0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1em0 ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1em0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1em0 OCA], [http://www.ebi.ac.uk/pdbsum/1em0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1em0 RCSB]</span>
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__TOC__
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}}
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</StructureSection>
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[[Category: Large Structures]]
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'''COMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN'''
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[[Category: Bennett M]]
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[[Category: Garman E]]
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[[Category: Krah A]]
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==Overview==
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[[Category: McKenna R]]
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The crystal structure of a B-type DNA hexanucleotide duplex complexed with the porphyrin molecule nickel-[tetra-N-methyl-pyridyl] porphyrin has been solved by multiwavelength anomalous diffraction phasing and refined to an R factor of 11.5% at a resolution of 0.9 A. The structure has been solved and refined as two crystallographically independent duplexes, stacked end to end. Contrary to expectation, the porphyrin molecule is not intercalated into the duplex but is stacked onto the ends of the two-duplex stack. The porphyrin molecule is highly buckled as a consequence of the nickel coordination, which produces large changes in local DNA structure. A second mode of porphyrin binding is apparent as a consequence of crystal packing, which places the ligand in the minor groove of an adjacent duplex. This structure thus provides, to our knowledge, the first atomic visualization of minor-groove binding for a porphyrin molecule. The geometry of groove binding provides a ready explanation for porphyrin-induced DNA strand cleavage at deoxyribose residues.
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[[Category: Neidle S]]
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[[Category: Sanderson M]]
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==About this Structure==
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[[Category: Wien F]]
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1EM0 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=1EM0 OCA].
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==Reference==
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A DNA-porphyrin minor-groove complex at atomic resolution: the structural consequences of porphyrin ruffling., Bennett M, Krah A, Wien F, Garman E, McKenna R, Sanderson M, Neidle S, Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9476-81. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10920199 10920199]
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[[Category: Protein complex]]
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[[Category: Bennett, M.]]
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[[Category: Garman, E.]]
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[[Category: Krah, A.]]
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[[Category: McKenna, R.]]
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[[Category: Neidle, S.]]
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[[Category: Sanderson, M.]]
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[[Category: Wien, F.]]
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[[Category: dna distortion]]
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[[Category: groove binding]]
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[[Category: porphyrin]]
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[[Category: ruffling]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:05:17 2008''
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Current revision

COMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN

PDB ID 1em0

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