2dbe - Revision history

OCA at 09:18, 14 February 2024

2024-02-14T09:18:41Z

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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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [https://pdbe.org/2dbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [https://www.ebi.ac.uk/pdbsum/2dbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbe ProSAT]</span></td></tr>
 </table>
 __TOC__
 </StructureSection>

OCA at 18:42, 20 September 2023

2023-09-20T18:42:40Z

← Older revision		Revision as of 18:42, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DBE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DBE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRN:BERENIL'>BRN</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]] 2.5Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRN:BERENIL'>BRN</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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [https://pdbe.org/2dbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [https://www.ebi.ac.uk/pdbsum/2dbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbe 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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [https://pdbe.org/2dbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [https://www.ebi.ac.uk/pdbsum/2dbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbe ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Brown~~, D G~~]]		[[Category: Brown DG]]
	[[Category: Brown, T]]		[[Category: Brown T]]
	[[Category: Garman, E]]		[[Category: Garman E]]
	[[Category: Jenkins~~, T C~~]]		[[Category: Jenkins TC]]
	[[Category: Neidle, S]]		[[Category: Neidle S]]
	[[Category: Sanderson~~, M R~~]]		[[Category: Sanderson MR]]
	[[Category: Skelly~~, J V~~]]		[[Category: Skelly JV]]
	[[Category: Stuart~~, D I]]~~		[[Category: Stuart DI]]
	~~[[Category: B-dna]]~~
	~~[[Category: Complexed with drug]]~~
	~~[[Category: Dna]]~~
	~~[[Category: Double helix~~]]

OCA at 10:29, 8 December 2021

2021-12-08T10:29:13Z

← Older revision		Revision as of 10:29, 8 December 2021
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	<StructureSection load='2dbe' size='340' side='right'caption='[[2dbe]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2dbe' size='340' side='right'caption='[[2dbe]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DBE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DBE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRN:BERENIL'>BRN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRN:BERENIL'>BRN</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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [~~http~~://pdbe.org/2dbe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dbe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbe 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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [https://pdbe.org/2dbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [https://www.ebi.ac.uk/pdbsum/2dbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbe ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:00, 4 March 2020

2020-03-04T08:00:50Z

← Older revision		Revision as of 08:00, 4 March 2020
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	==CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING==		==CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING==
	<StructureSection load='2dbe' size='340' side='right' caption='[[2dbe]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2dbe' size='340' side='right'caption='[[2dbe]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DBE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DBE FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Brown, D G]]		[[Category: Brown, D G]]
	[[Category: Brown, T]]		[[Category: Brown, T]]

OCA at 06:56, 30 May 2018

2018-05-30T06:56:03Z

← Older revision		Revision as of 06:56, 30 May 2018
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING==		==CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING==
	<StructureSection load='2dbe' size='340' side='right' caption='[[2dbe]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2dbe' size='340' side='right' caption='[[2dbe]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DBE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DBE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRN:BERENIL'>BRN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRN:BERENIL'>BRN</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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [http://pdbe.org/2dbe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [http://www.ebi.ac.uk/pdbsum/2dbe 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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [http://pdbe.org/2dbe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [http://www.ebi.ac.uk/pdbsum/2dbe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbe ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:01, 10 September 2015

2015-09-10T03:01:06Z

← Older revision		Revision as of 03:01, 10 September 2015
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	<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DBE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DBE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRN:BERENIL'>BRN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRN:BERENIL'>BRN</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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [http://www.ebi.ac.uk/pdbsum/2dbe 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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [http://pdbe.org/2dbe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [http://www.ebi.ac.uk/pdbsum/2dbe PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 2dbe" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:18, 15 January 2015

2015-01-15T17:18:51Z

← Older revision		Revision as of 17:18, 15 January 2015
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Brown, D G.]]		[[Category: Brown, D G]]
	[[Category: Brown, T.]]		[[Category: Brown, T]]
	[[Category: Garman, E.]]		[[Category: Garman, E]]
	[[Category: Jenkins, T C.]]		[[Category: Jenkins, T C]]
	[[Category: Neidle, S.]]		[[Category: Neidle, S]]
	[[Category: Sanderson, M R.]]		[[Category: Sanderson, M R]]
	[[Category: Skelly, J V.]]		[[Category: Skelly, J V]]
	[[Category: Stuart, D I.]]		[[Category: Stuart, D I]]
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Complexed with drug]]		[[Category: Complexed with drug]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]

OCA at 15:40, 12 October 2014

2014-10-12T15:40:23Z

← Older revision		Revision as of 15:40, 12 October 2014
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	[[~~Image~~:2dbe.~~png\|left\|200px~~]]		==CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING==
			<StructureSection load='2dbe' size='340' side='right' caption='[[2dbe]], [[Resolution\|resolution]] 2.50Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DBE FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRN:BERENIL'>BRN</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=2dbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dbe RCSB], [http://www.ebi.ac.uk/pdbsum/2dbe PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The three-dimensional structure of a complex between the dodecanucleotide d(CGCGAATTCGCG) and the anti-trypanocidal drug berenil, has been determined to a resolution of 2.5 A. The structure has been solved by molecular replacement and refined to an R factor of 0.177. A total of 49 water molecules have been located. The drug is bound at the 5'-AAT-3' region of the oligonucleotide. At one end of the drug the amidinium group is in hydrogen-bonded contact with N3 of the adenine base complementary to the thymine of the AAT. The other amidinium group does not make direct interactions with the DNA. Instead, a water molecule mediates between them. This is in hydrogen-bonded contact with an amidinium nitrogen atom, N3 of the 5' end adenine base and the ring oxygen atom of an adjacent deoxyribose. Molecular mechanics calculations have been performed on this complex, with the drug at various positions along the sequence. These show that the observed position is only 0.8 kcal/mol higher in energy than the best position. It is suggested that there is a broad energy well in the AATT region for this drug, and that water molecules as well as the neighbouring sequence, will determine precise positioning. More general aspects of minor groove binding are discussed.

	~~{{STRUCTURE_2dbe\| PDB=2dbe \| SCENE= }}~~		Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding.,Brown DG, Sanderson MR, Skelly JV, Jenkins TC, Brown T, Garman E, Stuart DI, Neidle S EMBO J. 1990 Apr;9(4):1329-34. PMID:2323343<ref>PMID:2323343</ref>

	~~===CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_2323343}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2dbe]] is~~ a ~~2 chain structure. Full crystallographic information is available from [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=2DBE OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018798655<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Brown, D G.]]		[[Category: Brown, D G.]]
	[[Category: Brown, T.]]		[[Category: Brown, T.]]

OCA: Protected "2dbe" [edit=sysop:move=sysop]

2013-01-06T11:29:22Z

Protected "2dbe" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:29, 6 January 2013
(No difference)

OCA at 11:29, 6 January 2013

2013-01-06T11:29:20Z

← Older revision		Revision as of 11:29, 6 January 2013
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	~~{{Seed}}~~
	[[Image:2dbe.png\|left\|200px]]		[[Image:2dbe.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2dbe", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2dbe\| PDB=2dbe \| SCENE= }}		{{STRUCTURE_2dbe\| PDB=2dbe \| SCENE= }}

	===CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING===		===CRYSTAL STRUCTURE OF A BERENIL-DODECANUCLEOTIDE COMPLEX: THE ROLE OF WATER IN SEQUENCE-SPECIFIC LIGAND BINDING===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_2323343}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 2323343 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_2323343}}		{{ABSTRACT_PUBMED_2323343}}

	==About this Structure==		==About this Structure==
	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA].		[[2dbe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBE OCA].

	==Reference==		==Reference==
	Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding., Brown DG, Sanderson MR, Skelly JV, Jenkins TC, Brown T, Garman E, Stuart DI, Neidle S, EMBO J. 1990 Apr;9(4):1329-34. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~2323343 2323343]~~		<ref group="xtra">PMID:018798655</ref><references group="xtra"/>
	[[Category: Brown, D G.]]		[[Category: Brown, D G.]]
	[[Category: Brown, T.]]		[[Category: Brown, T.]]
Line 34:		Line 22:
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Complexed with drug]]		[[Category: Complexed with drug]]
			[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 17:43:11 2008''~~