1d43: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1d43]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D43 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D43 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1d43]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D43 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D43 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HT:2-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>HT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HT:2-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5-BI-BENZIMIDAZOLE'>HT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1d43 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d43 OCA], [https://pdbe.org/1d43 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d43 RCSB], [https://www.ebi.ac.uk/pdbsum/1d43 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d43 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=1d43 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d43 OCA], [https://pdbe.org/1d43 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d43 RCSB], [https://www.ebi.ac.uk/pdbsum/1d43 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d43 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of the complex of Hoechst 33258 and the DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G has been solved from X-ray data collected at three different low temperatures (0, -25, and -100 degrees C). Such temperatures have permitted collection of higher resolution data (2.0, 1.9, and 2.0 A, respectively) than with previous X-ray studies of the same complex. In all three cases, the drug is located in the narrow central A-A-T-T region of the minor groove. Data analyses at -25 and -100 degrees C (each with a 1:1 drug/DNA ratio in the crystallizing solution) suggest a unique orientation for the drug. In contrast, two orientations of the drug were found equally possible at 0 degrees C with a 2:1 drug/DNA ratio in solution. Dihedral angles between the rings of Hoechst 33258 appear to change in a temperature-dependent manner. The drug/DNA complex is stabilized by single or bifurcated hydrogen bonds between the two N-H hydrogen-bond donors in the benzimidazole rings of Hoechst and adenine N3 and thymine O2 acceptors in the minor groove. A general preference for AT regions is conferred by electrostatic potential and by narrowing of the walls of the groove. Local point-by-point AT specificity follows from close van der Waals contacts between ring hydrogen atoms in Hoechst 33258 and the C2 hydrogens of adenines. Replacement of one benzimidazole ring by purine in a longer chain analogue of Hoechst 33258 could make that particular site GC tolerant in the manner observed at imidazole substitution for pyrrole in lexitropsins.
Low-temperature crystallographic analyses of the binding of Hoechst 33258 to the double-helical DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G.,Quintana JR, Lipanov AA, Dickerson RE Biochemistry. 1991 Oct 22;30(42):10294-306. PMID:1718416<ref>PMID:1718416</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1d43" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
</StructureSection>

Latest revision as of 09:49, 7 February 2024

DNA DODECAMER C-G-C-G-A-A-T-T-C-G-C-G/HOECHST 33258 COMPLEX: 0 DEGREES C, PIPERAZINE UPDNA DODECAMER C-G-C-G-A-A-T-T-C-G-C-G/HOECHST 33258 COMPLEX: 0 DEGREES C, PIPERAZINE UP

Structural highlights

1d43 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 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1d43, resolution 2.00Å

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