1em0

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==COMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN==
==COMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN==
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<StructureSection load='1em0' size='340' side='right' caption='[[1em0]], [[Resolution|resolution]] 0.90&Aring;' scene=''>
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<StructureSection load='1em0' size='340' side='right'caption='[[1em0]], [[Resolution|resolution]] 0.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EM0 FirstGlance]. <br>
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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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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PNI:TETRA[N-METHYL-PYRIDYL]+PORPHYRIN-NICKEL'>PNI</scene><br>
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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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<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr>
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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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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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.rcsb.org/pdb/explore.do?structureId=1em0 RCSB], [http://www.ebi.ac.uk/pdbsum/1em0 PDBsum]</span></td></tr>
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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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<table>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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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:10920199<ref>PMID:10920199</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bennett, M.]]
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[[Category: Large Structures]]
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[[Category: Garman, E.]]
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[[Category: Bennett M]]
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[[Category: Krah, A.]]
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[[Category: Garman E]]
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[[Category: McKenna, R.]]
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[[Category: Krah A]]
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[[Category: Neidle, S.]]
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[[Category: McKenna R]]
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[[Category: Sanderson, M.]]
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[[Category: Neidle S]]
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[[Category: Wien, F.]]
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[[Category: Sanderson M]]
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[[Category: Dna]]
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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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Current revision

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

PDB ID 1em0

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