1d8g

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[[Image:1d8g.gif|left|200px]]
 
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==ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)==
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The line below this paragraph, containing "STRUCTURE_1d8g", creates the "Structure Box" on the page.
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<StructureSection load='1d8g' size='340' side='right'caption='[[1d8g]], [[Resolution|resolution]] 0.74&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1d8g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D8G FirstGlance]. <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]] 0.74&#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=CA:CALCIUM+ION'>CA</scene></td></tr>
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{{STRUCTURE_1d8g| PDB=1d8g | SCENE= }}
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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=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [https://pdbe.org/1d8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [https://www.ebi.ac.uk/pdbsum/1d8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d8g ProSAT]</span></td></tr>
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</table>
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'''ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Ding S]]
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The affinity and specificity of a ligand for its DNA site is a function of the conformational changes between the isolated and complexed states. Although the structures of a hydroxypyrrole-imidazole-pyrrole polyamide dimer with 5'-CCAGTACTGG-3' and the trp repressor recognizing the sequence 5'-GTACT-3' are known, the baseline conformation of the DNA site would contribute to our understanding of DNA recognition by these ligands. The 0.74 A resolution structure of a B-DNA double helix, 5'-CCAGTACTGG-3', has been determined by X-ray crystallography. Six of the nine phosphates, two of four bound calcium ions and networks of water molecules hydrating the oligonucleotide have alternate conformations. By contrast, nine of the ten bases have a single, unique conformation with hydrogen atoms visible in most cases. The polyamide molecules alter the geometry of the phosphodiester backbone, and the water molecules mediating contacts in the trp repressor/operator complex are conserved in the unliganded DNA. Furthermore, the multiple conformational states, ions and hydration revealed by this ultrahigh resolution structure of a B-form oligonucleotide are potentially general considerations for understanding DNA-binding affinity and specificity by ligands.
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[[Category: Kielkopf CL]]
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[[Category: Kuhn P]]
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==About this Structure==
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[[Category: Rees DC]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D8G OCA].
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==Reference==
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Conformational flexibility of B-DNA at 0.74 A resolution: d(CCAGTACTGG)(2)., Kielkopf CL, Ding S, Kuhn P, Rees DC, J Mol Biol. 2000 Feb 25;296(3):787-801. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10677281 10677281]
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[[Category: Ding, S.]]
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[[Category: Kielkopf, C. L.]]
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[[Category: Kuhn, P.]]
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[[Category: Rees, D. C.]]
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[[Category: Alternate conformation]]
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[[Category: B-dna]]
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[[Category: Calcium]]
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[[Category: Polyamide]]
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[[Category: Trp repressor]]
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[[Category: Ultrahigh resolution]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:34:07 2008''
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Current revision

ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)

PDB ID 1d8g

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