1d30: Difference between revisions

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<StructureSection load='1d30' size='340' side='right'caption='[[1d30]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='1d30' size='340' side='right'caption='[[1d30]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1d30]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D30 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D30 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1d30]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D30 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAP:6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE'>DAP</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]] 2.4&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d30 OCA], [http://pdbe.org/1d30 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d30 RCSB], [http://www.ebi.ac.uk/pdbsum/1d30 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d30 ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAP:6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE'>DAP</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=1d30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d30 OCA], [https://pdbe.org/1d30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d30 RCSB], [https://www.ebi.ac.uk/pdbsum/1d30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d30 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structure of the DNA fluorochrome 4'-6-diamidine-2-phenyl indole (DAPI) bound to the synthetic B-DNA oligonucleotide C-G-C-G-A-A-T-T-C-G-C-G has been solved by single crystal x-ray diffraction methods, at a resolution of 2.4 A. The structure is nearly isomorphous with that of the native DNA molecule alone. With one DAPI and 25 waters per DNA double helix, the residual error is 21.5% for the 2428 reflections above the 2-sigma level. DAPI inserts itself edgewise into the narrow minor groove, displacing the ordered spine of hydration. DAPI and a single water molecule together span the four AT base pairs at the center of the duplex. The indole nitrogen forms a bifurcated hydrogen bond with the thymine O2 atoms of the two central base pairs, as with netropsin and Hoechst 33258. The preference of all three of these drugs for AT regions of B-DNA is a consequence of three factors: (1) The intrinsically narrower minor groove in AT regions than in GC regions of B-DNA, leading to a snug fit of the flat aromatic drug rings between the walls of the groove. (2) The more negative electrostatic potential within the minor groove in AT regions, attributable in part to the absence of electropositive-NH2 groups along the floor of the groove, and (3) The steric advantage of the absence of those same guanine-NH2 groups, thus permitting the drug molecule to sink deeper into the groove. Groove width and electrostatic factors are regional, and define the relative receptiveness of a section of DNA since they operate over several contiguous base pairs. The steric factor is local, varying from one base pair to the next, and hence is the means of fine-tuning sequence specificity.
The structure of DAPI bound to DNA.,Larsen TA, Goodsell DS, Cascio D, Grzeskowiak K, Dickerson RE J Biomol Struct Dyn. 1989 Dec;7(3):477-91. PMID:2627296<ref>PMID:2627296</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1d30" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cascio, D]]
[[Category: Cascio D]]
[[Category: Dickerson, R E]]
[[Category: Dickerson RE]]
[[Category: Goodsell, D S]]
[[Category: Goodsell DS]]
[[Category: Grzeskowiak, K]]
[[Category: Grzeskowiak K]]
[[Category: Larsen, T]]
[[Category: Larsen T]]
[[Category: B-dna]]
[[Category: Complexed with drug]]
[[Category: Dna]]
[[Category: Double helix]]

Latest revision as of 09:48, 7 February 2024

THE STRUCTURE OF DAPI BOUND TO DNATHE STRUCTURE OF DAPI BOUND TO DNA

Structural highlights

1d30 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 2.4Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1d30, resolution 2.40Å

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