3u05: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3u05]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U05 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3u05]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U05 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=804:6-(1,4,5,6-TETRAHYDROPYRIMIDIN-2-YL)-2-[4-(1,4,5,6-TETRAHYDROPYRIMIDIN-2-YL)BIPHENYL-4-YL]-1H-INDOLE'>804</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]] 1.27&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3u08|3u08]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=804:6-(1,4,5,6-TETRAHYDROPYRIMIDIN-2-YL)-2-[4-(1,4,5,6-TETRAHYDROPYRIMIDIN-2-YL)BIPHENYL-4-YL]-1H-INDOLE'>804</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=3u05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u05 OCA], [https://pdbe.org/3u05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u05 RCSB], [https://www.ebi.ac.uk/pdbsum/3u05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u05 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=3u05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u05 OCA], [https://pdbe.org/3u05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u05 RCSB], [https://www.ebi.ac.uk/pdbsum/3u05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u05 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported. A highly conserved cluster of 11 linked water molecules has been found in the native and all 3 ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing noncovalently binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by, hydrogen bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA.
Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster.,Wei D, Wilson WD, Neidle S J Am Chem Soc. 2013 Jan 30;135(4):1369-77. doi: 10.1021/ja308952y. Epub 2013 Jan , 16. PMID:23276263<ref>PMID:23276263</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3u05" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Neidle, S]]
[[Category: Neidle S]]
[[Category: Wei, D G]]
[[Category: Wei DG]]
[[Category: A2t2]]
[[Category: Db1804]]
[[Category: Dickerson and drew dodecamer]]
[[Category: Dna]]
[[Category: Dna minor groove binder]]
[[Category: Dna minor groove-ligand complex]]
[[Category: Double helix]]
[[Category: Mg2+]]
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