1d8g - Revision history

OCA at 06:50, 7 February 2024

2024-02-07T06:50:31Z

←Older revision		Revision as of 06:50, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<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>		<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>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 0.74Å</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>
	<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>		<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>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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.
-
-	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:10677281<ref>PMID:10677281</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1d8g" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ding, S]]	+	[[Category: Ding S]]
-	[[Category: Kielkopf~~, C L~~]]	+	[[Category: Kielkopf CL]]
-	[[Category: Kuhn, P]]	+	[[Category: Kuhn P]]
-	[[Category: Rees~~, D C]]~~	+	[[Category: Rees DC]]
-	~~[[Category: Alternate conformation]]~~	+
-	~~[[Category: B-dna]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Polyamide]]~~	+
-	~~[[Category: Trp repressor]]~~	+
-	~~[[Category: Ultrahigh resolution~~]]	+

OCA at 10:08, 22 June 2022

2022-06-22T10:08:38Z

←Older revision		Revision as of 10:08, 22 June 2022
Line 3:		Line 3:
	<StructureSection load='1d8g' size='340' side='right'caption='[[1d8g]], [[Resolution\|resolution]] 0.74Å' scene=''>		<StructureSection load='1d8g' size='340' side='right'caption='[[1d8g]], [[Resolution\|resolution]] 0.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<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 [~~http~~://proteopedia.org/fgij/fg.htm?mol=1D8G FirstGlance]. <br>	+	<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>
	</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>		</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>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [~~http~~://pdbe.org/1d8g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1d8g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1d8g ProSAT]</span></td></tr>	+	<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>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:31, 16 September 2020

2020-09-16T10:31:54Z

←Older revision		Revision as of 10:31, 16 September 2020
Line 1:		Line 1:

	==ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)==		==ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)==
-	<StructureSection load='1d8g' size='340' side='right' caption='[[1d8g]], [[Resolution\|resolution]] 0.74Å' scene=''>	+	<StructureSection load='1d8g' size='340' side='right'caption='[[1d8g]], [[Resolution\|resolution]] 0.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<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 [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1D8G FirstGlance]. <br>	+	<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 [http://proteopedia.org/fgij/fg.htm?mol=1D8G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</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>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [http://pdbe.org/1d8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [http://www.ebi.ac.uk/pdbsum/1d8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d8g ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [http://pdbe.org/1d8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [http://www.ebi.ac.uk/pdbsum/1d8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d8g ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ding, S]]		[[Category: Ding, S]]
	[[Category: Kielkopf, C L]]		[[Category: Kielkopf, C L]]

OCA at 11:15, 1 February 2017

2017-02-01T11:15:53Z

←Older revision		Revision as of 11:15, 1 February 2017
Line 1:		Line 1:
		+
	==ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)==		==ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)==
	<StructureSection load='1d8g' size='340' side='right' caption='[[1d8g]], [[Resolution\|resolution]] 0.74Å' scene=''>		<StructureSection load='1d8g' size='340' side='right' caption='[[1d8g]], [[Resolution\|resolution]] 0.74Å' scene=''>
Line 4:		Line 5:
	<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D8G FirstGlance]. <br>		<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D8G FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [http://pdbe.org/1d8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [http://www.ebi.ac.uk/pdbsum/1d8g PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [http://pdbe.org/1d8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [http://www.ebi.ac.uk/pdbsum/1d8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1d8g ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Ding, S]]		[[Category: Ding, S]]
-	[[Category: Kielkopf, C. L]]	+	[[Category: Kielkopf, C L]]
	[[Category: Kuhn, P]]		[[Category: Kuhn, P]]
-	[[Category: Rees, D. C]]	+	[[Category: Rees, D C]]
	[[Category: Alternate conformation]]		[[Category: Alternate conformation]]
	[[Category: B-dna]]		[[Category: B-dna]]

OCA at 18:14, 10 September 2015

2015-09-10T18:14:35Z

←Older revision		Revision as of 18:14, 10 September 2015
Line 4:		Line 4:
	<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D8G FirstGlance]. <br>		<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D8G FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [http://www.ebi.ac.uk/pdbsum/1d8g PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [http://pdbe.org/1d8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [http://www.ebi.ac.uk/pdbsum/1d8g PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1d8g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:50, 22 December 2014

2014-12-22T20:50:56Z

←Older revision		Revision as of 20:50, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D8G FirstGlance]. <br>		<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D8G FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<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=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [http://www.ebi.ac.uk/pdbsum/1d8g PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [http://www.ebi.ac.uk/pdbsum/1d8g PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ding, S.]]	+	[[Category: Ding, S]]
-	[[Category: Kielkopf, C. L.]]	+	[[Category: Kielkopf, C. L]]
-	[[Category: Kuhn, P.]]	+	[[Category: Kuhn, P]]
-	[[Category: Rees, D. C.]]	+	[[Category: Rees, D. C]]
	[[Category: Alternate conformation]]		[[Category: Alternate conformation]]
	[[Category: B-dna]]		[[Category: B-dna]]

OCA at 06:48, 4 September 2014

2014-09-04T06:48:57Z

←Older revision		Revision as of 06:48, 4 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1d8g.~~png~~\|~~left\|200px~~]]	+	==ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)==
		+	<StructureSection load='1d8g' size='340' side='right' caption='[[1d8g]], [[Resolution\|resolution]] 0.74Å' scene=''>
		+	== Structural highlights ==
		+	<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D8G FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<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=1d8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1d8g RCSB], [http://www.ebi.ac.uk/pdbsum/1d8g PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~{{STRUCTURE_1d8g\| PDB=1d8g \| SCENE= }}~~	+	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:10677281<ref>PMID:10677281</ref>

-	~~===ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10677281}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[1d8g]] is a 1 chain structure. Full crystallographic information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=1D8G OCA].~~	+	</StructureSection>
	[[Category: Ding, S.]]		[[Category: Ding, S.]]
	[[Category: Kielkopf, C. L.]]		[[Category: Kielkopf, C. L.]]

OCA: Protected "1d8g" [edit=sysop:move=sysop]

2012-10-21T20:53:21Z

Protected "1d8g" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:53, 21 October 2012

OCA at 20:53, 21 October 2012

2012-10-21T20:53:19Z

←Older revision		Revision as of 20:53, 21 October 2012
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-	{{Seed}}
	[[Image:1d8g.png\|left\|200px]]		[[Image:1d8g.png\|left\|200px]]

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	{{STRUCTURE_1d8g\| PDB=1d8g \| SCENE= }}		{{STRUCTURE_1d8g\| PDB=1d8g \| SCENE= }}

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

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	{{ABSTRACT_PUBMED_10677281}}		{{ABSTRACT_PUBMED_10677281}}

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D8G OCA].	+	[[1d8g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D8G OCA].
-		+
-	~~==Reference==~~	+
-	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]	+
	[[Category: Ding, S.]]		[[Category: Ding, S.]]
	[[Category: Kielkopf, C. L.]]		[[Category: Kielkopf, C. L.]]
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	[[Category: Alternate conformation]]		[[Category: Alternate conformation]]
	[[Category: B-dna]]		[[Category: B-dna]]
-	[[Category: ~~Calcium~~]]	+	[[Category: Dna]]
	[[Category: Polyamide]]		[[Category: Polyamide]]
	[[Category: Trp repressor]]		[[Category: Trp repressor]]
	[[Category: Ultrahigh resolution]]		[[Category: Ultrahigh resolution]]
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-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:40:16 2008''

OCA at 19:40, 30 June 2008

2008-06-30T19:40:18Z

←Older revision		Revision as of 19:40, 30 June 2008
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	{{STRUCTURE_1d8g\| PDB=1d8g \| SCENE= }}		{{STRUCTURE_1d8g\| PDB=1d8g \| SCENE= }}

-	~~'''~~ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)~~'''~~	+	===ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)===


-	~~==Overview==~~	+	<!--
-	~~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.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_10677281}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 10677281 is the PubMed ID number.
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		+	{{ABSTRACT_PUBMED_10677281}}

	==About this Structure==		==About this Structure==
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	[[Category: Trp repressor]]		[[Category: Trp repressor]]
	[[Category: Ultrahigh resolution]]		[[Category: Ultrahigh resolution]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May 2 13~~:34:07 2008''	+
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