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| - | [[Image:195d.gif|left|200px]] | |
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| - | <!--
| + | ==X-RAY STRUCTURES OF THE B-DNA DODECAMER D(CGCGTTAACGCG) WITH AN INVERTED CENTRAL TETRANUCLEOTIDE AND ITS NETROPSIN COMPLEX== |
| - | The line below this paragraph, containing "STRUCTURE_195d", creates the "Structure Box" on the page.
| + | <StructureSection load='195d' size='340' side='right'caption='[[195d]], [[Resolution|resolution]] 2.30Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[195d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=195D FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | -->
| + | <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> |
| - | {{STRUCTURE_195d| PDB=195d | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=195d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=195d OCA], [https://pdbe.org/195d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=195d RCSB], [https://www.ebi.ac.uk/pdbsum/195d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=195d ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''X-RAY STRUCTURES OF THE B-DNA DODECAMER D(CGCGTTAACGCG) WITH AN INVERTED CENTRAL TETRANUCLEOTIDE AND ITS NETROPSIN COMPLEX'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Balendiran K]] |
| - | The crystal structures of the B-DNA dodecamer d(CGCGTTAACGCG) duplex (T2A2), with the inverted tetranucleotide core from the duplex d(CGCGAATTCGCG) [A2T2, Dickerson & Drew (1981). J. Mol. Biol. 149, 761-768], and its netropsin complex (T2A2-N) have been determined at 2.3 A resolution. The crystals are orthorhombic, space group P2(1)2(1)2(1), unit-cell dimensions of a = 25.7, b = 40.5 and c = 67.0 A, for T2A2 and a = 25.49, b = 40.87, c = 67.02 A for T2A2-N and are isomorphous with A2T2. The native T2A2 structure, with 70 water molecules had a final R value of 0.15 for 1522 reflections (F > 2sigma), while for the netropsin complex, with 87 water molecules, the R value was 0.16 for 2420 reflections. In T2A2, a discontinuous string of zig-zagging water molecules hydrate the narrow A.T minor groove. In T2A2-N, netropsin binds in one orientation in the minor groove, covering the TTAA central region, by displacing the string of waters, forming the majority of hydrogen bonds with DNA atoms in one strand, and causing very little perturbation of the native structure. The helical twist angle in T2A2 is largest at the duplex center, corresponding to the cleavage site by the restriction enzymes HpaI and HincII. The sequence inversion AATT-->TTAA of the tetranucleotide at the center of the molecule results in a different path for the local helix axis in T2A2 and A2T2 but the overall bending is similar in both cases.
| + | [[Category: Rao ST]] |
| - | | + | [[Category: Sekharudu CY]] |
| - | ==About this Structure== | + | [[Category: Sundaralingam M]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=195D OCA]. | + | [[Category: Zon G]] |
| - | | + | |
| - | ==Reference== | + | |
| - | X-ray structures of the B-DNA dodecamer d(CGCGTTAACGCG) with an inverted central tetranucleotide and its netropsin complex., Balendiran K, Rao ST, Sekharudu CY, Zon G, Sundaralingam M, Acta Crystallogr D Biol Crystallogr. 1995 Mar 1;51(Pt 2):190-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15299320 15299320] | + | |
| - | [[Category: Balendiran, K.]] | + | |
| - | [[Category: Rao, S T.]]
| + | |
| - | [[Category: Sekharudu, C Y.]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: Zon, G.]] | + | |
| - | [[Category: B-dna]] | + | |
| - | [[Category: Complexed with drug]] | + | |
| - | [[Category: Double helix]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:35:28 2008''
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