1rqy

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[[Image:1rqy.gif|left|200px]]
[[Image:1rqy.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 1rqy |SIZE=350|CAPTION= <scene name='initialview01'>1rqy</scene>, resolution 1.55&Aring;
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The line below this paragraph, containing "STRUCTURE_1rqy", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=7AD:9-AMINO-N-[3-(DIMETHYLAMINO)PROPYL]ACRIDINE-4-CARBOXAMIDE'>7AD</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</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>
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|ACTIVITY=
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|GENE=
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|DOMAIN=
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{{STRUCTURE_1rqy| PDB=1rqy | SCENE= }}
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|RELATEDENTRY=[[1fn1|1FN1]], [[1fn2|1FN2]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rqy OCA], [http://www.ebi.ac.uk/pdbsum/1rqy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rqy RCSB]</span>
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'''9-amino-[N-(2-dimethylamino)proply]-acridine-4-carboxamide bound to d(CGTACG)2'''
'''9-amino-[N-(2-dimethylamino)proply]-acridine-4-carboxamide bound to d(CGTACG)2'''
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==About this Structure==
==About this Structure==
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1RQY 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=1RQY OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RQY OCA].
==Reference==
==Reference==
Structure of 9-amino-[N-(2-dimethylamino)propyl]acridine-4-carboxamide bound to d(CGTACG)(2): a comparison of structures of d(CGTACG)(2) complexed with intercalatorsin the presence of cobalt., Adams A, Guss JM, Denny WA, Wakelin LP, Acta Crystallogr D Biol Crystallogr. 2004 May;60(Pt 5):823-8. Epub 2004, Apr 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15103127 15103127]
Structure of 9-amino-[N-(2-dimethylamino)propyl]acridine-4-carboxamide bound to d(CGTACG)(2): a comparison of structures of d(CGTACG)(2) complexed with intercalatorsin the presence of cobalt., Adams A, Guss JM, Denny WA, Wakelin LP, Acta Crystallogr D Biol Crystallogr. 2004 May;60(Pt 5):823-8. Epub 2004, Apr 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15103127 15103127]
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[[Category: Protein complex]]
 
[[Category: Adams, A.]]
[[Category: Adams, A.]]
[[Category: Denny, W A.]]
[[Category: Denny, W A.]]
[[Category: Guss, J M.]]
[[Category: Guss, J M.]]
[[Category: Wakelin, L P.]]
[[Category: Wakelin, L P.]]
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[[Category: acridine]]
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[[Category: Acridine]]
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[[Category: b-dna]]
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[[Category: B-dna]]
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[[Category: cytosine exchange]]
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[[Category: Cytosine exchange]]
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[[Category: quadruplex]]
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[[Category: Quadruplex]]
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[[Category: unusual intercalation]]
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[[Category: Unusual intercalation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:48:40 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:31:50 2008''
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Revision as of 04:48, 3 May 2008

Image:1rqy.gif

Template:STRUCTURE 1rqy

9-amino-[N-(2-dimethylamino)proply]-acridine-4-carboxamide bound to d(CGTACG)2


Overview

The structure of the complex formed between 9-amino-[N-(2-dimethylamino)propyl]acridine-4-carboxamide and d(CGTACG)(2) has been refined to a resolution of 1.55 A. The complex crystallized in space group C222. An asymmetric unit comprises two strands of DNA, one disordered drug molecule, two cobalt(II) ions, two magnesium ions and 32 water molecules. The DNA helices stack in continuous columns, with their four central base pairs adopting a B-like motif. The terminal G.C base pairs engage in 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. An intercalation complex is formed involving four DNA duplexes, four disordered 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 stabilized by guanine N7-cobalt(II) coordination. The structure is compared with previously published isomorphous structures of d(CGTACG)(2) complexed with intercalators in the presence of cobalt and it is concluded that the formation of this crystal form is primarily determined by DNA-DNA interactions and packing forces, rather than by special interactions between the ligand and the DNA. Given the nature of the ligands found in these complexes, the relevance of the quadruplex structure to the biological activity of those agents, known to be topoisomerase poisons, is questioned.

About this Structure

Full crystallographic information is available from OCA.

Reference

Structure of 9-amino-[N-(2-dimethylamino)propyl]acridine-4-carboxamide bound to d(CGTACG)(2): a comparison of structures of d(CGTACG)(2) complexed with intercalatorsin the presence of cobalt., Adams A, Guss JM, Denny WA, Wakelin LP, Acta Crystallogr D Biol Crystallogr. 2004 May;60(Pt 5):823-8. Epub 2004, Apr 21. PMID:15103127 Page seeded by OCA on Sat May 3 07:48:40 2008

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