1em0
From Proteopedia
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|PDB= 1em0 |SIZE=350|CAPTION= <scene name='initialview01'>1em0</scene>, resolution 0.9Å | |PDB= 1em0 |SIZE=350|CAPTION= <scene name='initialview01'>1em0</scene>, resolution 0.9Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> | + | |LIGAND= <scene name='pdbligand=CBR:5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>CBR</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PNI:TETRA[N-METHYL-PYRIDYL]+PORPHYRIN-NICKEL'>PNI</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |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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[[Category: Sanderson, M.]] | [[Category: Sanderson, M.]] | ||
[[Category: Wien, F.]] | [[Category: Wien, F.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: PNI]] | ||
[[Category: dna distortion]] | [[Category: dna distortion]] | ||
[[Category: groove binding]] | [[Category: groove binding]] | ||
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[[Category: ruffling]] | [[Category: ruffling]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:05:17 2008'' |
Revision as of 17:05, 30 March 2008
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| , resolution 0.9Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
COMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN
Overview
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.
About this Structure
1EM0 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
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
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