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[[Image:1d8g.gif|left|200px]]<br /><applet load="1d8g" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1d8g, resolution 0.74&Aring;" />
'''ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)'''<br />


==Overview==
==ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)==
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.
<StructureSection load='1d8g' size='340' side='right'caption='[[1d8g]], [[Resolution|resolution]] 0.74&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<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>
1D8G is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D8G 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]] 0.74&#8491;</td></tr>
 
<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>
==Reference==
<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>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10677281 10677281]
</table>
[[Category: Protein complex]]
__TOC__
[[Category: Ding, S.]]
</StructureSection>
[[Category: Kielkopf, C. L.]]
[[Category: Large Structures]]
[[Category: Kuhn, P.]]
[[Category: Ding S]]
[[Category: Rees, D. C.]]
[[Category: Kielkopf CL]]
[[Category: CA]]
[[Category: Kuhn P]]
[[Category: alternate conformation]]
[[Category: Rees DC]]
[[Category: b-dna]]
[[Category: calcium]]
[[Category: polyamide]]
[[Category: trp repressor]]
[[Category: ultrahigh resolution]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:14:04 2008''

Latest revision as of 09:50, 7 February 2024

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

Structural highlights

1d8g is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 0.74Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1d8g, resolution 0.74Å

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