1k2z
From Proteopedia
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|PDB= 1k2z |SIZE=350|CAPTION= <scene name='initialview01'>1k2z</scene>, resolution 2.38Å | |PDB= 1k2z |SIZE=350|CAPTION= <scene name='initialview01'>1k2z</scene>, resolution 2.38Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=DMY:DISTAMYCIN A'>DMY</scene> | + | |LIGAND= <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=DMY:DISTAMYCIN+A'>DMY</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k2z OCA], [http://www.ebi.ac.uk/pdbsum/1k2z PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1k2z RCSB]</span> | ||
}} | }} | ||
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[[Category: Meervelt, L Van.]] | [[Category: Meervelt, L Van.]] | ||
[[Category: Uytterhoeven, K.]] | [[Category: Uytterhoeven, K.]] | ||
| - | [[Category: DMY]] | ||
[[Category: b-dna double helix]] | [[Category: b-dna double helix]] | ||
[[Category: base triplet]] | [[Category: base triplet]] | ||
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[[Category: minor groove binding]] | [[Category: minor 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 21:42:38 2008'' |
Revision as of 18:42, 30 March 2008
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| , resolution 2.38Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The Crystal Structure of d(GGCCAATTGG) Complexed with Distamycin.
Overview
Single-crystal X-ray structure determinations of the complex between the minor-groove binder distamycin and d(GGCCAATTGG) reveal two 1 : 1 binding modes which differ in the orientation of the drug molecule in the minor groove. The two crystals were grown from different crystallization conditions and found to diffract to 2.38 and 1.85 A, respectively. The structures were refined to completion using SHELXL-93, resulting in a residual R factor of 20.30% for the 2.38-A resolution structure (including 46 water molecules) and 19.74% for the 1.85-A resolution structure (including 74 water molecules). In both orientations, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and AT base pairs. With a binding site of at least five base pairs, close contacts between the terminal distamycin atoms and guanine amino groups are inevitable. The detailed nature of several of these interactions was further investigated by ab initio quantum chemical methods.
About this Structure
1K2Z is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG)., Uytterhoeven K, Sponer J, Van Meervelt L, Eur J Biochem. 2002 Jun;269(12):2868-77. PMID:12071949
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