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306d

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SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICITACIC)

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Retrieved from "http://52.214.119.220/wiki/index.php/306d"

Categories: Large Structures | Chen X | Ramakrishnan B | Sundaralingam M

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-[[Image:306d.gif|left|200px]]<br /><applet load="306d" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="306d, resolution 1.600&Aring;" />
-'''SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICITACIC)'''<br />
-==Overview==
+==SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICITACIC)==
-To understand the recognition interactions between AT-containing, alternating DNA and minor groove binding drugs, the crystal structures of, the side-by-side binding of two distamycin molecules to the DNA octamers, d(ICITACIC)2 and d(ICATATIC)2, referred to here as TA and ATAT, respectively, have been determined at 1.6 A and 2.2 A, respectively., Compared to the previous 2:1 all-IC d(ICICICIC)2-distamycin complex, the, substitutions of the I x C base-pairs by the A x T base-pairs enable the, interactions of the drug with its natural target to be studied. Both, complexes assume side-by-side drug binding, isomorphous to the all IC, counterpart in the tetragonal space group P4(1)22 (a = b = 28.03 A, c =, 58.04 A and a = b = 27.86 A, c = 58.62 A, respectively). The ATAT complex, also crystallized in a new polymorphic monoclinic space group C2 (a =, 33.38 A, b = 25.33 A, c = 28.11 A and beta = 120.45 degrees) and was, solved at 1.9 A resolution. The structures of the three double drug x DNA, complexes are very similar, characterized by systematic hydrogen bonding, and van der Waals interactions. Each drug hydrogen bonds with the bases of, the proximal DNA strand only and stacks with the sugar moiety, while the, side-by-side drugs themselves exhibit pyrrole ring-peptide stacking. The, pyrrole-peptide interaction is crucial for the side-by-side binding mode, of the distamycin/netropsin family of drugs. The purine-pyrimidine, alternation is probably responsible for the striking alternation in the, helical and backbone conformations. The structures are conserved between, the pure IC complex and the AT substituted complexes but further details, of the side-by-side binding to DNA are provided by the 1.6 A resolution, structure of TA.
+<StructureSection load='306d' size='340' side='right'caption='[[306d]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[306d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=306D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=306D FirstGlance]. <br>
-D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=DMY:'>DMY</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=306D OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMY:DISTAMYCIN+A'>DMY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=306d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=306d OCA], [https://pdbe.org/306d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=306d RCSB], [https://www.ebi.ac.uk/pdbsum/306d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=306d ProSAT]</span></td></tr>
-Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC)., Chen X, Ramakrishnan B, Sundaralingam M, J Mol Biol. 1997 Apr 18;267(5):1157-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9150404 9150404]
+</table>
-[[Category: Protein complex]]
+__TOC__
-[[Category: Chen, X.]]
+</StructureSection>
-[[Category: Ramakrishnan, B.]]
+[[Category: Large Structures]]
-[[Category: Sundaralingam, M.]]
+[[Category: Chen X]]
-[[Category: DMY]]
+[[Category: Ramakrishnan B]]
-[[Category: MG]]
+[[Category: Sundaralingam M]]
-[[Category: b-dna]]
-[[Category: complexed with drug]]
-[[Category: double drug in the minor groove]]
-[[Category: double helix]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 21:34:36 2008''

306d

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SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICITACIC)

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