1dnz - Revision history

OCA at 06:56, 7 February 2024

OCA — Wed, 07 Feb 2024 06:56:53 GMT

←Older revision		Revision as of 06:56, 7 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNZ 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]] 1.6Å</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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [https://pdbe.org/1dnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [https://www.ebi.ac.uk/pdbsum/1dnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnz 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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [https://pdbe.org/1dnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [https://www.ebi.ac.uk/pdbsum/1dnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnz ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Magnesium ions play important roles in the structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding to tight places where phosphates are clustered, the molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions at high resolution. The structures reveal that A-form nucleic acid has characteristic [Mg(H(2)O)(6)](2+)binding modes. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH(3))(6)](3+), a model ion of [Mg(H(2)O)(6)](2+), binds in an identical manner. The other mode involves the binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove. These [Mg(H(2)O)(6)](2+)ions are found at the most negative electrostatic potential regions of A-form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A-form duplexes.
-
-	Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.,Robinson H, Gao YG, Sanishvili R, Joachimiak A, Wang AH Nucleic Acids Res. 2000 Apr 15;28(8):1760-6. PMID:10734195<ref>PMID:10734195</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1dnz" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:37, 14 December 2022

OCA — Wed, 14 Dec 2022 10:37:06 GMT

←Older revision		Revision as of 10:37, 14 December 2022
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNZ 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d1b\|1d1b]], [[212d\|212d]], [[221d\|221d]]</div></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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [https://pdbe.org/1dnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [https://www.ebi.ac.uk/pdbsum/1dnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnz 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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [https://pdbe.org/1dnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [https://www.ebi.ac.uk/pdbsum/1dnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnz ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gao, Y G]]	+	[[Category: Gao Y-G]]
-	[[Category: Joachimiak, A]]	+	[[Category: Joachimiak A]]
-	[[Category: Robinson, H]]	+	[[Category: Robinson H]]
-	[[Category: Sanishvili, R]]	+	[[Category: Sanishvili R]]
-	[[Category: Wang~~, A H.~~J]]	+	[[Category: Wang AH-J]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna conformation]]~~	+
-	~~[[Category: Metal ion~~]]	+

OCA at 18:31, 10 March 2021

OCA — Wed, 10 Mar 2021 18:31:32 GMT

←Older revision		Revision as of 18:31, 10 March 2021
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	<StructureSection load='1dnz' size='340' side='right'caption='[[1dnz]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1dnz' size='340' side='right'caption='[[1dnz]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DNZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNZ 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d1b\|1d1b]], [[212d\|212d]], [[221d\|221d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1d1b\|1d1b]], [[212d\|212d]], [[221d\|221d]]</div></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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [~~http~~://pdbe.org/1dnz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1dnz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnz 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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [https://pdbe.org/1dnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [https://www.ebi.ac.uk/pdbsum/1dnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:59, 5 June 2019

OCA — Wed, 05 Jun 2019 23:59:33 GMT

←Older revision		Revision as of 23:59, 5 June 2019
Line 1:		Line 1:

	==A-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES==		==A-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES==
-	<StructureSection load='1dnz' size='340' side='right' caption='[[1dnz]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1dnz' size='340' side='right'caption='[[1dnz]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DNZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DNZ FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Gao, Y G]]		[[Category: Gao, Y G]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 04:03, 30 August 2017

OCA — Wed, 30 Aug 2017 04:03:46 GMT

←Older revision		Revision as of 04:03, 30 August 2017
Line 1:		Line 1:
		+
	==A-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES==		==A-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES==
	<StructureSection load='1dnz' size='340' side='right' caption='[[1dnz]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1dnz' size='340' side='right' caption='[[1dnz]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 5:		Line 6:
	</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d1b\|1d1b]], [[212d\|212d]], [[221d\|221d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d1b\|1d1b]], [[212d\|212d]], [[221d\|221d]]</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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [http://pdbe.org/1dnz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [http://www.ebi.ac.uk/pdbsum/1dnz 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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [http://pdbe.org/1dnz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [http://www.ebi.ac.uk/pdbsum/1dnz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:09, 11 September 2015

OCA — Fri, 11 Sep 2015 01:09:12 GMT

←Older revision		Revision as of 01:09, 11 September 2015
Line 5:		Line 5:
	</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d1b\|1d1b]], [[212d\|212d]], [[221d\|221d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d1b\|1d1b]], [[212d\|212d]], [[221d\|221d]]</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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [http://www.ebi.ac.uk/pdbsum/1dnz 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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [http://pdbe.org/1dnz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [http://www.ebi.ac.uk/pdbsum/1dnz PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		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 1dnz" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:27, 22 December 2014

OCA — Mon, 22 Dec 2014 06:27:45 GMT

←Older revision		Revision as of 06:27, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DNZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DNZ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d1b\|1d1b]], [[212d\|212d]], [[221d\|221d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d1b\|1d1b]], [[212d\|212d]], [[221d\|221d]]</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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [http://www.ebi.ac.uk/pdbsum/1dnz 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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [http://www.ebi.ac.uk/pdbsum/1dnz 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 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Gao, Y G.]]	+	[[Category: Gao, Y G]]
-	[[Category: Joachimiak, A.]]	+	[[Category: Joachimiak, A]]
-	[[Category: Robinson, H.]]	+	[[Category: Robinson, H]]
-	[[Category: Sanishvili, R.]]	+	[[Category: Sanishvili, R]]
-	[[Category: Wang, A H.J.]]	+	[[Category: Wang, A H.J]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Dna conformation]]		[[Category: Dna conformation]]
	[[Category: Metal ion]]		[[Category: Metal ion]]

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

OCA — Sun, 08 Jun 2014 05:32:41 GMT

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

←Older revision

Revision as of 05:32, 8 June 2014

OCA at 05:32, 8 June 2014

OCA — Sun, 08 Jun 2014 05:32:37 GMT

←Older revision		Revision as of 05:32, 8 June 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==A-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES==
-	[[~~Image:~~1dnz.~~png~~\|~~left~~\|~~200px~~]]	+	<StructureSection load='1dnz' size='340' side='right' caption='[[1dnz]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1dnz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DNZ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1d1b\|1d1b]], [[212d\|212d]], [[221d\|221d]]</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=1dnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dnz RCSB], [http://www.ebi.ac.uk/pdbsum/1dnz PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Magnesium ions play important roles in the structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding to tight places where phosphates are clustered, the molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions at high resolution. The structures reveal that A-form nucleic acid has characteristic [Mg(H(2)O)(6)](2+)binding modes. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH(3))(6)](3+), a model ion of [Mg(H(2)O)(6)](2+), binds in an identical manner. The other mode involves the binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove. These [Mg(H(2)O)(6)](2+)ions are found at the most negative electrostatic potential regions of A-form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A-form duplexes.

-	<!--	+	Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.,Robinson H, Gao YG, Sanishvili R, Joachimiak A, Wang AH Nucleic Acids Res. 2000 Apr 15;28(8):1760-6. PMID:10734195<ref>PMID:10734195</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_1dnz"~~, ~~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_1dnz\| PDB=1dnz \| SCENE= }}~~	+

-	~~===A-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_10734195}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 10734195 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_10734195}}~~	+
-		+
-	==~~About this Structure~~==	+
-	~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1DNZ OCA].~~	+
-		+
-	~~==Reference==~~	+
-	Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes., Robinson H, Gao YG, Sanishvili R, Joachimiak A, Wang AH, Nucleic Acids Res. 2000 Apr 15;28(8):1760-6. PMID:[http:/~~/www.ncbi.nlm.nih.gov/pubmed/10734195 10734195]~~	+
	[[Category: Gao, Y G.]]		[[Category: Gao, Y G.]]
	[[Category: Joachimiak, A.]]		[[Category: Joachimiak, A.]]
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	[[Category: Sanishvili, R.]]		[[Category: Sanishvili, R.]]
	[[Category: Wang, A H.J.]]		[[Category: Wang, A H.J.]]
		+	[[Category: Dna]]
	[[Category: Dna conformation]]		[[Category: Dna conformation]]
	[[Category: Metal ion]]		[[Category: Metal ion]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 23:21:14 2008''

OCA at 20:21, 30 June 2008

OCA — Mon, 30 Jun 2008 20:21:16 GMT

←Older revision		Revision as of 20:21, 30 June 2008
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-	[[Image:1dnz.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1dnz.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1dnz\| PDB=1dnz \| SCENE= }}		{{STRUCTURE_1dnz\| PDB=1dnz \| SCENE= }}

-	~~'''~~A-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES~~'''~~	+	===A-DNA DECAMER ACCGGCCGGT WITH MAGNESIUM BINDING SITES===


-	~~==Overview==~~	+	<!--
-	~~Magnesium ions play important roles in~~ the ~~structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding~~ to ~~tight places where phosphates are clustered,~~ the ~~molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d~~(~~ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions~~ at ~~high resolution~~. ~~The structures reveal that A-form nucleic acid has characteristic [Mg(H(2)O)(6)](2+)binding modes~~. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH(3))(6)](3+), ~~a model ion of [Mg(H(2)O)(6)](2+), binds in an identical manner. The other mode involves~~ the ~~binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove~~. ~~These [Mg(H(2)O)(6)](2+)ions are found at the most negative electrostatic potential regions of A~~-~~form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A~~-~~form duplexes.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_10734195}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 10734195 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_10734195}}

	==About this Structure==		==About this Structure==
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	[[Category: Dna conformation]]		[[Category: Dna conformation]]
	[[Category: Metal ion]]		[[Category: Metal ion]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May 2 14~~:04:06 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 23:21:14 2008''