3dnb - Revision history

OCA at 12:44, 26 July 2023

OCA — Wed, 26 Jul 2023 12:44:47 GMT

←Older revision		Revision as of 12:44, 26 July 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DNB FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DNB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [https://pdbe.org/3dnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB], [https://www.ebi.ac.uk/pdbsum/3dnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dnb 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=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [https://pdbe.org/3dnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB], [https://www.ebi.ac.uk/pdbsum/3dnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dnb ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dickerson~~, R E~~]]	+	[[Category: Dickerson RE]]
-	[[Category: Prive~~, G G]]~~	+	[[Category: Prive GG]]
-	~~[[Category: B-dna]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Double helix]]~~	+
-	~~[[Category: Mismatched~~]]	+

OCA at 08:29, 25 May 2022

OCA — Wed, 25 May 2022 08:29:06 GMT

←Older revision		Revision as of 08:29, 25 May 2022
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	<StructureSection load='3dnb' size='340' side='right'caption='[[3dnb]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='3dnb' size='340' side='right'caption='[[3dnb]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3DNB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DNB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [~~http~~://pdbe.org/3dnb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dnb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dnb 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=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [https://pdbe.org/3dnb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB], [https://www.ebi.ac.uk/pdbsum/3dnb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dnb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:00, 19 August 2020

OCA — Wed, 19 Aug 2020 07:00:15 GMT

←Older revision		Revision as of 07:00, 19 August 2020
Line 1:		Line 1:

	==HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER==		==HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER==
-	<StructureSection load='3dnb' size='340' side='right' caption='[[3dnb]], [[Resolution\|resolution]] 1.30Å' scene=''>	+	<StructureSection load='3dnb' size='340' side='right'caption='[[3dnb]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DNB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3DNB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [http://pdbe.org/3dnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB], [http://www.ebi.ac.uk/pdbsum/3dnb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dnb 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=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [http://pdbe.org/3dnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB], [http://www.ebi.ac.uk/pdbsum/3dnb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dnb 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: Dickerson, R E]]		[[Category: Dickerson, R E]]
	[[Category: Prive, G G]]		[[Category: Prive, G G]]

OCA at 17:06, 11 August 2016

OCA — Thu, 11 Aug 2016 17:06:51 GMT

←Older revision		Revision as of 17:06, 11 August 2016
Line 1:		Line 1:
		+
	==HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER==		==HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER==
	<StructureSection load='3dnb' size='340' side='right' caption='[[3dnb]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='3dnb' size='340' side='right' caption='[[3dnb]], [[Resolution\|resolution]] 1.30Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[3dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DNB FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DNB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB], [http://www.ebi.ac.uk/pdbsum/3dnb 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=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [http://pdbe.org/3dnb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB], [http://www.ebi.ac.uk/pdbsum/3dnb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dnb ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 3dnb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:17, 12 November 2014

OCA — Wed, 12 Nov 2014 08:17:25 GMT

←Older revision		Revision as of 08:17, 12 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3dnb.~~png~~\|~~left\|200px~~]]	+	==HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER==
		+	<StructureSection load='3dnb' size='340' side='right' caption='[[3dnb]], [[Resolution\|resolution]] 1.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DNB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB], [http://www.ebi.ac.uk/pdbsum/3dnb PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the DNA decamer C-C-A-A-C-G-T-T-G-G has been solved to a resolution of 1.4 A, and is compared with the 1.3 A structure of C-C-A-A-G-A-T-T-G-G and the 1.6 A structure of C-C-A-G-G-C-C-T-G-G. All three decamers crystallize isomorphously in space group C2 with five base-pairs per asymmetric unit, and with decamer double helices stacked atop one another along the c axis in a manner that closely approximates a continuous B helix. This efficient stacking probably accounts for the high resolution of the crystal data. Comparison of the three decamers reveals the following. (1) Minor groove width is more variable than heretofore realized. Regions of A.T base-pairs tend to be narrower than average, although two successive A.T base-pairs alone may not be sufficient to produce narrowing. The minor groove is wider in regions where BII phosphate conformations are opposed diagonally across the groove. (2) Narrow regions of minor groove exhibit a zig-zag spine of hydration, as was first seen in C-G-C-G-A-A-T-T-C-G-C-G, whereas wide regions show two ribbons of water molecules down the walls, connecting base edge N or O with sugar O-4' atoms. Regions of intermediate groove width may accommodate neither pattern of hydration well, and may exhibit a less regular pattern of hydration. (3) Base-pair stacking is virtually identical at equivalent positions in the three decamers. The unconnected step from the top of one decamer helix to the bottom of the next helix is a normal helix step in all respects, except for the absence of connecting phosphate groups. (4) BII phosphate conformation require the unstacking of the two bases linked by the phosphate, but do not necessarily follow as an inevitable consequence of unstacking. They have an influence on minor groove width as noted in point (1) above. (5) Sugar ring pseudorotation P and main-chain torsion angle delta show an excellent correlation as given by the equation: delta = 40 degrees cos (P + 144 degrees) + 120 degrees. Although centered around C-2'-endo, the conformations in these B-DNA helices are distributed broadly from C-3'-exo to O-4'-endo, unlike the tighter clustering around C-3'-endo observed in A-DNA oligomer structures.

-	~~{{STRUCTURE_3dnb\| PDB=3dnb \| SCENE= }}~~	+	Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G.,Prive GG, Yanagi K, Dickerson RE J Mol Biol. 1991 Jan 5;217(1):177-99. PMID:1988677<ref>PMID:1988677</ref>

-	~~===HELIX GEOMETRY~~, ~~HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_1988677}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3dnb]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3DNB OCA].~~	+	</StructureSection>
-		+	[[Category: Dickerson, R E]]
-	==~~Reference~~==	+	[[Category: Prive, G G]]
-	<~~ref group="xtra">PMID:001988677<~~/~~ref~~><~~references group="xtra"~~/>	+
-	[[Category: Dickerson, R E.]]	+
-	[[Category: Prive, G G.]]	+
	[[Category: B-dna]]		[[Category: B-dna]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Mismatched]]		[[Category: Mismatched]]

OCA: Protected "3dnb" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 20:08:36 GMT

Protected "3dnb" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:08, 7 January 2013

OCA at 20:08, 7 January 2013

OCA — Mon, 07 Jan 2013 20:08:34 GMT

←Older revision		Revision as of 20:08, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3dnb.png\|left\|200px]]		[[Image:3dnb.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3dnb", 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_3dnb\| PDB=3dnb \| SCENE= }}		{{STRUCTURE_3dnb\| PDB=3dnb \| SCENE= }}

	===HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER===		===HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_1988677}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 1988677 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_1988677}}		{{ABSTRACT_PUBMED_1988677}}

	==About this Structure==		==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA].	+	[[3dnb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA].

	==Reference==		==Reference==
-	Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G., Prive GG, Yanagi K, Dickerson RE, J Mol Biol. 1991 Jan 5;217(1):177-99. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~1988677 1988677]~~	+	<ref group="xtra">PMID:001988677</ref><references group="xtra"/>
	[[Category: Dickerson, R E.]]		[[Category: Dickerson, R E.]]
	[[Category: Prive, G G.]]		[[Category: Prive, G G.]]
	[[Category: B-dna]]		[[Category: B-dna]]
		+	[[Category: Dna]]
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Mismatched]]		[[Category: Mismatched]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 10:00:36 2008''

OCA at 07:00, 28 July 2008

OCA — Mon, 28 Jul 2008 07:00:37 GMT

←Older revision		Revision as of 07:00, 28 July 2008
Line 1:		Line 1:
-	[[Image:3dnb.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3dnb.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_3dnb\| PDB=3dnb \| SCENE= }}		{{STRUCTURE_3dnb\| PDB=3dnb \| SCENE= }}

-	~~'''~~HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER~~'''~~	+	===HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER===


-	~~==Overview==~~	+	<!--
-	The ~~crystal structure of the DNA decamer C-C-A-A-C-G-T-T-G-G has been solved to a resolution of 1.4 A~~, and is compared with the 1.3 A structure of C-C-A-A-G-A-T-T-G-G and the 1.6 A structure of C-C-A-G-G-C-C-T-G-G. All three decamers crystallize isomorphously in space group C2 with five base-pairs per asymmetric unit, ~~and with decamer double helices stacked atop one another along~~ the c axis in a manner that closely approximates a continuous B helix. This efficient stacking probably accounts for the high resolution of the crystal data. Comparison of the three decamers reveals the following. (1) Minor groove width is more variable than heretofore realized. Regions of A.T base-pairs tend to be narrower than average, although two successive A.T base-pairs alone may not be sufficient to produce narrowing. The minor groove is wider in regions where BII phosphate conformations are opposed diagonally across the ~~groove.~~ (~~2) Narrow regions of minor groove exhibit a zig-zag spine of hydration,~~ as was first seen in C-G-C-G-A-A-T-T-C-G-C-G, whereas wide regions show two ribbons of water molecules down the walls, connecting base edge N or O with sugar O-4' atoms. Regions of intermediate groove width may accommodate neither pattern of hydration well, and may exhibit a less regular pattern of hydration. (3) Base-pair stacking is virtually identical at ~~equivalent positions in the three decamers~~. ~~The unconnected step from the top of one decamer helix to the bottom of the next helix is a normal helix step in all respects, except for the absence of connecting phosphate groups~~. (4) ~~BII phosphate conformation require the unstacking of the two bases linked by the phosphate~~, but do not necessarily follow as an inevitable consequence of unstacking. They have an influence on minor groove width as noted in point (1) above. (5) Sugar ring pseudorotation P and main-chain torsion angle delta show an excellent correlation as given by the ~~equation: delta = 40 degrees cos (P + 144 degrees) + 120 degrees~~. ~~Although centered around C~~-2'-~~endo, the conformations in these B-DNA helices are distributed broadly from C-3'-exo to O-4'-endo, unlike the tighter clustering around C-3'-endo observed in A-DNA oligomer structures.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_1988677}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 1988677 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_1988677}}

	==About this Structure==		==About this Structure==
Line 25:		Line 29:
	[[Category: Double helix]]		[[Category: Double helix]]
	[[Category: Mismatched]]		[[Category: Mismatched]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 22~~:00:19 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 10:00:36 2008''

OCA at 19:00, 4 May 2008

OCA — Sun, 04 May 2008 19:00:20 GMT

←Older revision		Revision as of 19:00, 4 May 2008
Line 1:		Line 1:
	[[Image:3dnb.gif\|left\|200px]]		[[Image:3dnb.gif\|left\|200px]]

-	{{Structure	+	<!--
-	\|PDB~~= 3dnb \|SIZE=350\|CAPTION= <~~scene ~~name='initialview01'>3dnb</scene>~~, ~~resolution 1~~.~~300Å~~	+	The line below this paragraph, containing "STRUCTURE_3dnb", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=DA:2'~~-~~DEOXYADENOSINE~~-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_3dnb\| PDB=3dnb \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [http://www.ebi.ac.uk/pdbsum/3dnb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB]</span>	+
-	}}	+

	'''HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER'''		'''HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER'''
Line 19:		Line 16:

	==About this Structure==		==About this Structure==
-	~~3DNB is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA].	+	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DNB OCA].

	==Reference==		==Reference==
	Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G., Prive GG, Yanagi K, Dickerson RE, J Mol Biol. 1991 Jan 5;217(1):177-99. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1988677 1988677]		Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G., Prive GG, Yanagi K, Dickerson RE, J Mol Biol. 1991 Jan 5;217(1):177-99. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1988677 1988677]
-	[[Category: Protein complex]]
	[[Category: Dickerson, R E.]]		[[Category: Dickerson, R E.]]
	[[Category: Prive, G G.]]		[[Category: Prive, G G.]]
-	[[Category: b-dna]]	+	[[Category: B-dna]]
-	[[Category: ~~double~~ helix]]	+	[[Category: Double helix]]
-	[[Category: ~~mismatched~~]]	+	[[Category: Mismatched]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:00:19 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:32:57 2008''	+

OCA at 02:32, 31 March 2008

OCA — Mon, 31 Mar 2008 02:32:59 GMT

←Older revision		Revision as of 02:32, 31 March 2008
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	\|PDB= 3dnb \|SIZE=350\|CAPTION= <scene name='initialview01'>3dnb</scene>, resolution 1.300Å		\|PDB= 3dnb \|SIZE=350\|CAPTION= <scene name='initialview01'>3dnb</scene>, resolution 1.300Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>	+	\|LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3dnb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dnb OCA], [http://www.ebi.ac.uk/pdbsum/3dnb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3dnb RCSB]</span>
	}}		}}

Line 23:		Line 26:
	[[Category: Dickerson, R E.]]		[[Category: Dickerson, R E.]]
	[[Category: Prive, G G.]]		[[Category: Prive, G G.]]
-	[[Category: MG]]
	[[Category: b-dna]]		[[Category: b-dna]]
	[[Category: double helix]]		[[Category: double helix]]
	[[Category: mismatched]]		[[Category: mismatched]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:04:24 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:32:57 2008''