1d45: Difference between revisions

Revision as of 13:25, 2 May 2008

DNA DODECAMER C-G-C-G-A-A-T-T-C-G-C-G/HOECHST 33258 COMPLEX:-25 DEGREES C, PIPERAZINE DOWN

OverviewOverview

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.

About this StructureAbout this Structure

Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Fri May 2 13:25:55 2008

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OCA

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 [[Image:1d45.gif|left|200px]]
- {{Structure
+<!--
-|PDB= 1d45 |SIZE=350|CAPTION= <scene name='initialview01'>1d45</scene>, resolution 1.900&Aring;
+The line below this paragraph, containing "STRUCTURE_1d45", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=HT:2&#39;-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5&#39;-BI-BENZIMIDAZOLE'>HT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
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+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_1d45|  PDB=1d45  |  SCENE=  }}
-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d45 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d45 OCA], [http://www.ebi.ac.uk/pdbsum/1d45 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d45 RCSB]</span>
-}}
 '''DNA DODECAMER C-G-C-G-A-A-T-T-C-G-C-G/HOECHST 33258 COMPLEX:-25 DEGREES C, PIPERAZINE DOWN'''
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 ==About this Structure==
-D45 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D45 OCA].
+Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D45 OCA].
 ==Reference==
 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:[http://www.ncbi.nlm.nih.gov/pubmed/1718416 1718416]
-[[Category: Protein complex]]
 [[Category: Dickerson, R E.]]
 [[Category: Lipanov, A A.]]
 [[Category: Quintana, J R.]]
-[[Category: b-dna]]
+[[Category: B-dna]]
-[[Category: complexed with drug]]
+[[Category: Complexed with drug]]
-[[Category: double helix]]
+[[Category: Double helix]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:25:55 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:34:19 2008''