1fn2
From Proteopedia
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|PDB= 1fn2 |SIZE=350|CAPTION= <scene name='initialview01'>1fn2</scene>, resolution 1.60Å | |PDB= 1fn2 |SIZE=350|CAPTION= <scene name='initialview01'>1fn2</scene>, resolution 1.60Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=8AD:9-AMINO-(N-(2-DIMETHYLAMINO)BUTYL)ACRIDINE-4-CARBOXAMIDE'>8AD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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=NA:SODIUM+ION'>NA</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fn2 OCA], [http://www.ebi.ac.uk/pdbsum/1fn2 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1fn2 RCSB]</span> | ||
}} | }} | ||
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[[Category: Guss, J M.]] | [[Category: Guss, J M.]] | ||
[[Category: Wakelin, L P.G.]] | [[Category: Wakelin, L P.G.]] | ||
| - | [[Category: 8AD]] | ||
| - | [[Category: CO]] | ||
| - | [[Category: NA]] | ||
[[Category: acridine-4-carboxamide]] | [[Category: acridine-4-carboxamide]] | ||
[[Category: dna]] | [[Category: dna]] | ||
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[[Category: quadruplex]] | [[Category: quadruplex]] | ||
| - | ''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 20:26:10 2008'' |
Revision as of 17:26, 30 March 2008
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| , resolution 1.60Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
9-AMINO-(N-(2-DIMETHYLAMINO)BUTYL)ACRIDINE-4-CARBOXAMIDE BOUND TO D(CGTACG)2
Overview
The structures of the complexes formed between 9-amino-[N:-(2-dimethyl-amino)butyl]acridine-4-carboxamide and d(CG(5Br)UACG)(2) and d(CGTACG)(2) have been solved by X-ray crystallography using MAD phasing methodology and refined to a resolution of 1.6 A. The complexes crystallised in space group C222. An asymmetric unit in the brominated complex comprises two strands of DNA, one disordered drug molecule, two cobalt (II) ions and 19 water molecules (31 in the native complex). Asymmetric units in the native complex also contain a sodium ion. The structures exhibit novel features not previously observed in crystals of DNA/drug complexes. The DNA helices stack in continuous columns with their central 4 bp adopting a B-like motif. However, despite being a palindromic sequence, the terminal GC base pairs engage in quite different interactions. At one end of the duplex there is a CpG dinucleotide overlap modified by ligand intercalation and terminal cytosine exchange between symmetry-related duplexes. A novel intercalation complex is formed involving four DNA duplexes, four ligand molecules and two pairs of base tetrads. The other end of the DNA is frayed with the terminal guanine lying in the minor groove of the next duplex in the column. The structure is stabilised by guanine N7/cobalt (II) coordination. We discuss our findings with respect to the effects of packing forces on DNA crystal structure, and the potential effects of intercalating agents on biochemical processes involving DNA quadruplexes and strand exchanges. NDB accession numbers: DD0032 (brominated) and DD0033 (native).
About this Structure
1FN2 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
A novel form of intercalation involving four DNA duplexes in an acridine-4-carboxamide complex of d(CGTACG)(2)., Adams A, Guss JM, Collyer CA, Denny WA, Wakelin LP, Nucleic Acids Res. 2000 Nov 1;28(21):4244-53. PMID:11058124
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