454d
From Proteopedia
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|PDB= 454d |SIZE=350|CAPTION= <scene name='initialview01'>454d</scene>, resolution 1.2Å | |PDB= 454d |SIZE=350|CAPTION= <scene name='initialview01'>454d</scene>, resolution 1.2Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=RHM:DELTA-ALPHA-RH[2R,9R-DIAMINO-4,7-DIAZADECANE]9,10-PHENANTHRENEQUINONE DIIMINE'>RHM</scene> | + | |LIGAND= <scene name='pdbligand=5IU:5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>5IU</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=RHM:DELTA-ALPHA-RH[2R,9R-DIAMINO-4,7-DIAZADECANE]9,10-PHENANTHRENEQUINONE+DIIMINE'>RHM</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=454d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=454d OCA], [http://www.ebi.ac.uk/pdbsum/454d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=454d RCSB]</span> | ||
}} | }} | ||
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[[Category: Kielkopf, C L.]] | [[Category: Kielkopf, C L.]] | ||
[[Category: Rees, D C.]] | [[Category: Rees, D C.]] | ||
| - | [[Category: RHM]] | ||
[[Category: intercalation]] | [[Category: intercalation]] | ||
[[Category: major groove recognition]] | [[Category: major groove recognition]] | ||
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[[Category: photoexcitable]] | [[Category: photoexcitable]] | ||
| - | ''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 05:37:23 2008'' |
Revision as of 02:37, 31 March 2008
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| , resolution 1.2Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3'
Overview
Intercalating complexes of rhodium(III) are strong photo-oxidants that promote DNA strand cleavage or electron transfer through the double helix. The 1.2 A resolution crystal structure of a sequence-specific rhodium intercalator bound to a DNA helix provides a rationale for the sequence specificity of rhodium intercalators. It also explains how intercalation in the center of an oligonucleotide modifies DNA conformation. The rhodium complex intercalates via the major groove where specific contacts are formed with the edges of the bases at the target site. The phi ligand is deeply inserted into the DNA base pair stack. The primary conformational change of the DNA is a doubling of the rise per residue, with no change in sugar pucker from B-form DNA. Based upon the five crystallographically independent views of an intercalated DNA helix observed in this structure, the intercalator may be considered as an additional base pair with specific functional groups positioned in the major groove.
About this Structure
454D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of a photoactive rhodium complex intercalated into DNA., Kielkopf CL, Erkkila KE, Hudson BP, Barton JK, Rees DC, Nat Struct Biol. 2000 Feb;7(2):117-21. PMID:10655613
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