1d63

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[[Image:1d63.gif|left|200px]]
 
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==CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES==
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The line below this paragraph, containing "STRUCTURE_1d63", creates the "Structure Box" on the page.
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<StructureSection load='1d63' size='340' side='right'caption='[[1d63]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1d63]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D63 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRN:BERENIL'>BRN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_1d63| PDB=1d63 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d63 OCA], [https://pdbe.org/1d63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d63 RCSB], [https://www.ebi.ac.uk/pdbsum/1d63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d63 ProSAT]</span></td></tr>
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</table>
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'''CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Brown DG]]
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The AT-selective drug berenil has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The crystal structure has been solved to a resolution of 2.0 A and an R factor of 18.3%, with the location of 65 water molecules. The drug is symmetrically bound in the 5'-AATT region of the minor groove, with its amidinium groups hydrogen-bonding to O-2 atoms of the thymine base at each end of the binding site. This arrangement is distinct from that previously found for berenil with the sequence d(CGCGAATTCGCG)2, which has the drug bound to the sequencing 5'-ATT via hydrogen bonds to adenine N-3 atoms with the involvement of a bridging water molecule at one end of the binding site. The reasons for these differences are discussed in terms of changes in helical parameters; in particular propeller twist and base-pair roll are considered to be important. The conformational and base-pair geometry of the dodecanucleotide in the structure reported here, is closely similar to that for the native structure, suggesting that the 5'-AAATTT sequence does not significantly alter during drug binding, either because of its inflexibility or because its geometry is nearly ideal for berenil binding.
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[[Category: Garman E]]
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[[Category: Neidle S]]
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==About this Structure==
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[[Category: Sanderson MR]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D63 OCA].
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==Reference==
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Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features., Brown DG, Sanderson MR, Garman E, Neidle S, J Mol Biol. 1992 Jul 20;226(2):481-90. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1640462 1640462]
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[[Category: Brown, D G.]]
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[[Category: Garman, E.]]
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[[Category: Neidle, S.]]
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[[Category: Sanderson, M R.]]
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[[Category: B-dna]]
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[[Category: Complexed with drug]]
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[[Category: Double helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:29:38 2008''
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Current revision

CRYSTAL STRUCTURE OF A BERENIL-D(CGCAAATTTGCG) COMPLEX; AN EXAMPLE OF DRUG-DNA RECOGNITION BASED ON SEQUENCE-DEPENDENT STRUCTURAL FEATURES

PDB ID 1d63

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