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1d22

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BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO DNA: STRUCTURAL COMPARISON

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Categories: Large Structures | Gao Y-G | Liaw Y-C | Robinson H | Wang AH-J

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-[[Image:1d22.jpg|left|200px]]<br /><applet load="1d22" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1d22, resolution 1.800&Aring;" />
-'''BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO DNA: STRUCTURAL COMPARISON'''<br />
-==Overview==
+==BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO DNA: STRUCTURAL COMPARISON==
-The three-dimensional molecular structures of the complexes between a, novel antitumor drug nogalamycin and its derivative U-58872 with a, modified DNA hexamer d[m5CGT(pS)Am5CG] have been determined at 1.7- and, 1.8-A resolution, respectively, by X-ray diffraction analyses. Both, structures (in space group P6(1)) have been refined with constrained, refinement procedure to final R factors of 0.208 (3386 reflections) and, 0.196 (2143 reflections). In both complexes, two nogalamycins bind to the, DNA hexamer double helix in a 2:1 ratio with the elongated aglycon, chromophore intercalated between the CpG steps at both ends of the helix., The aglycon chromophore spans across the GC Watson-Crick base pairs with, its nogalose lying in the minor groove and the aminoglucose lying in the, major groove of the distorted B-DNA double helix. Most of the sugars, remain in the C2'-endo pucker family, except three deoxycytidine residues, (terminal C1, C7, and internal C5). All nucleotides are in the anti, conformation. Specific hydrogen bonds are found in the complex between the, drug and guanine-cytosine bases in both grooves of the helix. One hydroxyl, group of the aminoglucose donates a hydrogen bond to the N7 of guanine, while the other receives a hydrogen bond from the N4 amino group of, cytosine. The orientation of these two hydrogen bonds suggests that, nogalamycin prefers a GC base pair with its aglycon chromophore, intercalating at the 5'-side of a guanine (between NpG), or at the 3'-side, of a cytosine (between CpN) with the sugars pointing toward the GC base, pair. The binding of nogalamycin to DNA requires that the base pairs in, DNA open up transiently to allow the bulky sugars to go through, suggesting that nogalamycin prefers GC sequences embedded in a stretch of, AT sequences.
+<StructureSection load='1d22' size='340' side='right'caption='[[1d22]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1d22]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D22 FirstGlance]. <br>
-D22 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NGU as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D22 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene>, <scene name='pdbligand=NGU:U-58872,+HYDROXY+DERIVATIVE+OF+NOGALAMYCIN'>NGU</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=1d22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d22 OCA], [https://pdbe.org/1d22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d22 RCSB], [https://www.ebi.ac.uk/pdbsum/1d22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d22 ProSAT]</span></td></tr>
-Binding of the antitumor drug nogalamycin and its derivatives to DNA: structural comparison., Gao YG, Liaw YC, Robinson H, Wang AH, Biochemistry. 1990 Nov 13;29(45):10307-16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2261474 2261474]
+</table>
-[[Category: Protein complex]]
+__TOC__
-[[Category: Gao, Y.G.]]
+</StructureSection>
-[[Category: Liaw, Y.C.]]
+[[Category: Large Structures]]
-[[Category: Robinson, H.]]
+[[Category: Gao Y-G]]
-[[Category: Wang, A.H.J.]]
+[[Category: Liaw Y-C]]
-[[Category: NGU]]
+[[Category: Robinson H]]
-[[Category: complexed with drug]]
+[[Category: Wang AH-J]]
-[[Category: double helix]]
-[[Category: modified]]
-[[Category: right handed dna]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:17:43 2007''

1d22

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BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO DNA: STRUCTURAL COMPARISON

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