1dne

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(New page: 200px<br /><applet load="1dne" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dne, resolution 2.400&Aring;" /> '''MOLECULAR STRUCTURE...)
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[[Image:1dne.gif|left|200px]]<br /><applet load="1dne" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dne, resolution 2.400&Aring;" />
 
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'''MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2'''<br />
 
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==Overview==
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==MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2==
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The molecular structure of the complex between a minor groove binding drug, (netropsin) and the DNA dodecamer d(CGCGATATCGCG) has been solved and, refined by single-crystal X-ray diffraction analysis to a final R factor, of 20.0% to 2.4-A resolution. The crystal is similar to that of the other, related dodecamers with unit cell dimensions of a = 25.48 A, b = 41.26 A, and c = 66.88 A in the space group P2(1)2(1)2(1). In the complex, netropsin binds to the central ATAT tetranucleotide segment in the narrow, minor groove of the dodecamer B-DNA double helix as expected. However, in, the structural refinement the drug is found to fit the electron density in, two orientations equally well, suggesting the disordered model. This, agrees with the results from solution studies (chemical footprinting and, NMR) of the interactions between minor groove binding drugs (e.g., netropsin and distamycin A) and DNA. The stabilizing forces between drug, and DNA are provided by a combination of ionic, van der Waals, and, hydrogen-bonding interactions. No bifurcated hydrogen bond is found, between netropsin and DNA in this complex due to the unique dispositions, of the hydrogen-bond acceptors (N3 of adenine and O2 of thymine) on the, floor of the DNA minor groove. Two of the four AT base pairs in the ATAT, stretch have low propeller twist angles, even though the DNA has a narrow, minor groove. Alternating helical twist angles are observed in the ATAT, stretch with lower twist in the ApT steps than in the TpA step.
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<StructureSection load='1dne' size='340' side='right'caption='[[1dne]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1dne]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNE FirstGlance]. <br>
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1DNE is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NT as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DNE OCA].
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dne OCA], [https://pdbe.org/1dne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dne RCSB], [https://www.ebi.ac.uk/pdbsum/1dne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dne ProSAT]</span></td></tr>
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Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment., Coll M, Aymami J, van der Marel GA, van Boom JH, Rich A, Wang AH, Biochemistry. 1989 Jan 10;28(1):310-20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2539859 2539859]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Aymami, J.]]
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</StructureSection>
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[[Category: Boom, J.H.Van.]]
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[[Category: Large Structures]]
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[[Category: Coll, M.]]
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[[Category: Aymami J]]
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[[Category: Marel, G.A.Van.Der.]]
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[[Category: Coll M]]
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[[Category: Rich, A.]]
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[[Category: Rich A]]
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[[Category: Wang, A.H.J.]]
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[[Category: Van Boom JH]]
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[[Category: NT]]
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[[Category: Van Der Marel GA]]
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[[Category: b-dna]]
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[[Category: Wang AH-J]]
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[[Category: complexed with drug]]
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[[Category: double helix]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:22:35 2007''
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Current revision

MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2

PDB ID 1dne

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