1eg6
From Proteopedia
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|PDB= 1eg6 |SIZE=350|CAPTION= <scene name='initialview01'>1eg6</scene>, resolution 2.00Å | |PDB= 1eg6 |SIZE=350|CAPTION= <scene name='initialview01'>1eg6</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=3CO:COBALT+(III)+ION'>3CO</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene> | + | |LIGAND= <scene name='pdbligand=3CO:COBALT+(III)+ION'>3CO</scene>, <scene name='pdbligand=BFA:9-BROMO-PHENAZINE-1-CARBOXYLIC+ACID+(2-DIMETHYLAMINO-ETHYL)-AMIDE'>BFA</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</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=DU:2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>DU</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1eg6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eg6 OCA], [http://www.ebi.ac.uk/pdbsum/1eg6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1eg6 RCSB]</span> | ||
}} | }} | ||
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[[Category: Hobbs, J R.]] | [[Category: Hobbs, J R.]] | ||
[[Category: Thorpe, J H.]] | [[Category: Thorpe, J H.]] | ||
| - | [[Category: 3CO]] | ||
| - | [[Category: BFA]] | ||
| - | [[Category: BR]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: drug-dna complex]] | [[Category: drug-dna complex]] | ||
| Line 33: | Line 33: | ||
[[Category: major groove binding]] | [[Category: major groove binding]] | ||
| - | ''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 20:01:52 2008'' |
Revision as of 17:01, 30 March 2008
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| , resolution 2.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE ANALYSIS OF D(CG(5-BRU)ACG) COMPLEXES TO A PHENAZINE
Overview
The structure of the duplex d[CG(5-BrU)ACG](2) bound to 9-bromophenazine-4-carboxamide has been solved through MAD phasing at 2.0 A resolution. It shows an unexpected and previously unreported intercalation cavity stabilized by the drug and novel binding modes of Co(2+) ions at certain guanine N7 sites. For the intercalation cavity the terminal cytosine is rotated to pair with the guanine of a symmetry-related duplex to create a pseudo-Holliday junction geometry, with two such cavities linked through the minor groove interactions of the N2/N3 guanine sites at an angle of 40 degrees, creating a quadruplex-like structure. The mode of binding of the drug is shown to be disordered, with the major conformations showing the side chain bound to the N7 position of adjacent guanines. The other end of the duplex exhibits a terminal base fraying in the presence of Co(2+) ions linking symmetry-related guanines, causing the helices to intertwine through the minor groove. The stabilization of the structure by the intercalating drug shows that this class of compound may bind to DNA junctions as well as duplex DNA or to strand-nicked DNA ('hemi-intercalated'), as in the cleavable complex. This suggests a structural basis for the dual poisoning of topoisomerase I and II enzymes by this family of drugs.
About this Structure
1EG6 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Guanine specific binding at a DNA junction formed by d[CG(5-BrU)ACG](2) with a topoisomerase poison in the presence of Co(2+) ions., Thorpe JH, Hobbs JR, Todd AK, Denny WA, Charlton P, Cardin CJ, Biochemistry. 2000 Dec 12;39(49):15055-61. PMID:11106483
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