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1dne

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==MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2==
==MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2==
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<StructureSection load='1dne' size='340' side='right' caption='[[1dne]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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<StructureSection load='1dne' size='340' side='right'caption='[[1dne]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DNE FirstGlance]. <br>
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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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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NT:NETROPSIN'>NT</scene><br>
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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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dne OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dne RCSB], [http://www.ebi.ac.uk/pdbsum/1dne PDBsum]</span></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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<table>
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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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<div style="background-color:#fffaf0;">
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</table>
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== Publication Abstract from PubMed ==
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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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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:2539859<ref>PMID:2539859</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Aymami, J.]]
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[[Category: Large Structures]]
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[[Category: Boom, J H.Van.]]
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[[Category: Aymami J]]
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[[Category: Coll, M.]]
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[[Category: Coll M]]
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[[Category: Marel, G A.Van Der.]]
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[[Category: Rich A]]
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[[Category: Rich, A.]]
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[[Category: Van Boom JH]]
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[[Category: Wang, A H.J.]]
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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: Dna]]
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[[Category: Double helix]]
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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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