154d: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[154d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=154D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=154D FirstGlance]. <br>
<table><tr><td colspan='2'>[[154d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=154D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=154D FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLD:BIS-(N-ETHYLPYRIDINIUM-(3-METHOXYCARBAZOLE))HEXANE-1,6-DIAMINE'>FLD</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=FLD:BIS-(N-ETHYLPYRIDINIUM-(3-METHOXYCARBAZOLE))HEXANE-1,6-DIAMINE'>FLD</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=154d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=154d OCA], [https://pdbe.org/154d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=154d RCSB], [https://www.ebi.ac.uk/pdbsum/154d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=154d ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=154d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=154d OCA], [https://pdbe.org/154d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=154d RCSB], [https://www.ebi.ac.uk/pdbsum/154d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=154d ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The bis-intercalators Flexi-Di and ditercalinium are synthetic dimers that bis-intercalate into DNA and cause cell death in prokaryotes from futile and abortive repair of DNA. Each is composed of two 7H-pyridocarbazole units and a linker. Flexi-Di has a flexible spermine-like linker while ditercalinium has a rigid bis(ethylpiperidinium) linker. This report, describing the 2.5-A X-ray structure of Flexi-Di complexed with [d(BrCGCG)]2, appears to be the first report of a three-dimensional structure of a DNA complex with a bis-intercalator with a flexible linker. DNA complex formation with a ditercalinium analog having a flexible linker was not anticipated to yield unstacked and bent DNA as was observed in the previously reported ditercalinium.[d(CGCG)]2 complex. Surprisingly, the DNA in the Flexi-Di complex is bent to a degree exceeding that of the ditercalinium complex. A comparison of the DNA complexes of Flexi-Di and ditercalinium has allowed us to propose a mechanism by which these bis-intercalators distort DNA. We propose that this class of bis-intercalators pulls the internal base pairs into the major groove and pushes the external base pairs into the minor groove. The result is a bend toward the minor groove. It appears that hydrogen bonds between the linker and the internal guanines effectively pull the central base pairs of the complex out into the major groove. At the external regions of the complex, stacking interactions between the chromophores and terminal base pairs effectively push the terminal base pairs into the minor groove. The result of this push/pull combination is to bend the DNA.
DNA distortion in bis-intercalated complexes.,Peek ME, Lipscomb LA, Bertrand JA, Gao Q, Roques BP, Garbay-Jaureguiberry C, Williams LD Biochemistry. 1994 Apr 5;33(13):3794-800. PMID:8142381<ref>PMID:8142381</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 154d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bertrand, J A]]
[[Category: Bertrand JA]]
[[Category: Gao, Q]]
[[Category: Gao Q]]
[[Category: Garbay-Jaureguiberry, C]]
[[Category: Garbay-Jaureguiberry C]]
[[Category: Lipscomb, L A]]
[[Category: Lipscomb LA]]
[[Category: Peek, M E]]
[[Category: Peek ME]]
[[Category: Roques, B P]]
[[Category: Roques BP]]
[[Category: Williams, L D]]
[[Category: Williams LD]]
[[Category: Complexed with drug]]
[[Category: Dna]]
[[Category: Double helix]]
[[Category: Modified]]
[[Category: Right handed dna]]

Latest revision as of 09:25, 7 February 2024

DNA DISTORTION IN BIS-INTERCALATED COMPLEXESDNA DISTORTION IN BIS-INTERCALATED COMPLEXES

Structural highlights

154d is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

154d, resolution 2.50Å

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