360d
From Proteopedia
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|PDB= 360d |SIZE=350|CAPTION= <scene name='initialview01'>360d</scene>, resolution 1.850Å | |PDB= 360d |SIZE=350|CAPTION= <scene name='initialview01'>360d</scene>, resolution 1.850Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=BPF:2,5-BIS{[4-(N-ETHYLAMIDINO)]PHENYL}FURAN'>BPF</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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=360d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=360d OCA], [http://www.ebi.ac.uk/pdbsum/360d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=360d RCSB]</span> | ||
}} | }} | ||
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[[Category: Guerri, S Neidle A.]] | [[Category: Guerri, S Neidle A.]] | ||
[[Category: Simpson, I J.]] | [[Category: Simpson, I J.]] | ||
| - | [[Category: BPF]] | ||
| - | [[Category: MG]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: complexed with drug]] | [[Category: complexed with drug]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:47 2008'' |
Revision as of 02:21, 31 March 2008
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| , resolution 1.850Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF 2,5-BIS{[4-(N-ETHYLAMIDINO)PHENYL]}FURAN COMPLEXED TO 5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'. A MINOR GROOVE DRUG COMPLEX, SHOWING PATTERNS OF GROOVE HYDRATION
Overview
The crystal structure is reported of a complex between an ethyl derivative of the minor-groove drug furamidine and the dodecanucleotide duplex d(CGCGAATTCGCG)2, which has been refined to 1.85 A resolution and an R factor of 16.6% for data collected at -173 degreesC. An exceptionally large number (220) of water molecules have been located. The majority of these occur in the first coordination shell of solvation. There are extensive networks of connected waters, both in the major and minor grooves. In particular, there are 21 water molecules associated with the minor-groove drug, via hydrogen bonds from the four charged nitrogen atoms. One cluster of four waters is situated in the groove itself; the majority are on the outer edge of the groove, and serve to bridge between the outward-directed drug nitrogen atoms and backbone phosphate oxygen atoms. These bridges are both intra- and inter-strand, with the net effect that the outer edge of the drug molecule is covered by ribbons of water molecules.
About this Structure
360D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Visualisation of extensive water ribbons and networks in a DNA minor-groove drug complex., Guerri A, Simpson IJ, Neidle S, Nucleic Acids Res. 1998 Jun 15;26(12):2873-8. PMID:9611230
Page seeded by OCA on Mon Mar 31 05:21:47 2008
