5kie - Revision history

OCA at 07:25, 1 May 2024

OCA — Wed, 01 May 2024 07:25:02 GMT

←Older revision		Revision as of 07:25, 1 May 2024
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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=5kie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kie OCA], [https://pdbe.org/5kie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kie RCSB], [https://www.ebi.ac.uk/pdbsum/5kie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kie 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=5kie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kie OCA], [https://pdbe.org/5kie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kie RCSB], [https://www.ebi.ac.uk/pdbsum/5kie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kie ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Single ribonucleotide intrusions represent the most common non-standard nucleotide in genomic DNA, yet little is known of their structural impact. This lesion incurs genomic instability in addition to affecting the physical properties of the DNA.To probe for structural and dynamic effects of single ribonucleotides in various sequence contexts, AxC, CxG and GxC, where x=rG or dG, we report the structures of three single ribonucleotide containing DNA duplexes and the corresponding DNA controls. This lesion subtly and locally perturbs the structure asymmetrically 3' of the lesion on both the riboguanosine-containing and complementary strand of the duplex. The perturbations are mainly restricted to the sugar and phosphodiester backbone. The ribose and 3' downstream deoxyriboses are predominately in N-type conformation, while backbone torsion angles epsilon and/or zeta of the ribonucleotide or upstream deoxyribonucleotide are affected. Depending on the flanking sequences, the C2'-OH group forms hydrogen bonds with the backbone, 3'- neighboring base and/or sugar. Interestingly, even in a similar purine-rG-pyrimidine environment (A-rG-C and G-rG-C), a riboguanosine affects DNA in a distinct manner and manifests different hydrogen bonds, which makes generalizations difficult.
-
-	Structural impact of single ribonucleotides in DNA.,Evich M, Spring-Connell AM, Storici F, Germann MW Chembiochem. 2016 Aug 9. doi: 10.1002/cbic.201600385. PMID:27504600<ref>PMID:27504600</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5kie" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:47, 27 September 2023

OCA — Wed, 27 Sep 2023 10:47:30 GMT

←Older revision		Revision as of 10:47, 27 September 2023
Line 1:		Line 1:

	==Structural impact of single ribonucleotides in DNA==		==Structural impact of single ribonucleotides in DNA==
-	<StructureSection load='5kie' size='340' side='right'caption='[[5kie~~]], [[NMR_Ensembles_of_Models \| 3 NMR models~~]]' scene=''>	+	<StructureSection load='5kie' size='340' side='right'caption='[[5kie]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kie]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KIE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kie]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KIE FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5kgv\|5kgv]], [[5ki7\|5ki7]], [[5kib\|5kib]], [[5kif\|5kif]], [[5kih\|5kih]]~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=5kie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kie OCA], [~~http~~://pdbe.org/5kie PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kie RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kie PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kie 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=5kie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kie OCA], [https://pdbe.org/5kie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kie RCSB], [https://www.ebi.ac.uk/pdbsum/5kie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kie ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Evich, M]]	+	[[Category: Synthetic construct]]
-	[[Category: Germann~~, M W~~]]	+	[[Category: Evich M]]
-	[[Category: Spring-Connell~~, A M~~]]	+	[[Category: Germann MW]]
-	[[Category: Storici, F]]	+	[[Category: Spring-Connell AM]]
-	~~[[Category: Dna]]~~	+	[[Category: Storici F]]
-	~~[[Category: Ribonucleotide]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 15:26, 8 July 2020

OCA — Wed, 08 Jul 2020 15:26:11 GMT

←Older revision		Revision as of 15:26, 8 July 2020
Line 1:		Line 1:

	==Structural impact of single ribonucleotides in DNA==		==Structural impact of single ribonucleotides in DNA==
-	<StructureSection load='5kie' size='340' side='right' caption='[[5kie]], [[NMR_Ensembles_of_Models \| 3 NMR models]]' scene=''>	+	<StructureSection load='5kie' size='340' side='right'caption='[[5kie]], [[NMR_Ensembles_of_Models \| 3 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kie]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KIE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kie]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KIE FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kgv\|5kgv]], [[5ki7\|5ki7]], [[5kib\|5kib]], [[5kif\|5kif]], [[5kih\|5kih]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kgv\|5kgv]], [[5ki7\|5ki7]], [[5kib\|5kib]], [[5kif\|5kif]], [[5kih\|5kih]]</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=5kie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kie OCA], [http://pdbe.org/5kie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kie RCSB], [http://www.ebi.ac.uk/pdbsum/5kie PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kie 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=5kie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kie OCA], [http://pdbe.org/5kie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kie RCSB], [http://www.ebi.ac.uk/pdbsum/5kie PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kie 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: Evich, M]]		[[Category: Evich, M]]
	[[Category: Germann, M W]]		[[Category: Germann, M W]]

OCA at 06:54, 10 September 2016

OCA — Sat, 10 Sep 2016 06:54:29 GMT

←Older revision		Revision as of 06:54, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kie is ~~ON HOLD~~	+	==Structural impact of single ribonucleotides in DNA==
		+	<StructureSection load='5kie' size='340' side='right' caption='[[5kie]], [[NMR_Ensembles_of_Models \| 3 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kie]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KIE FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kgv\|5kgv]], [[5ki7\|5ki7]], [[5kib\|5kib]], [[5kif\|5kif]], [[5kih\|5kih]]</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=5kie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kie OCA], [http://pdbe.org/5kie PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kie RCSB], [http://www.ebi.ac.uk/pdbsum/5kie PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kie ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Single ribonucleotide intrusions represent the most common non-standard nucleotide in genomic DNA, yet little is known of their structural impact. This lesion incurs genomic instability in addition to affecting the physical properties of the DNA.To probe for structural and dynamic effects of single ribonucleotides in various sequence contexts, AxC, CxG and GxC, where x=rG or dG, we report the structures of three single ribonucleotide containing DNA duplexes and the corresponding DNA controls. This lesion subtly and locally perturbs the structure asymmetrically 3' of the lesion on both the riboguanosine-containing and complementary strand of the duplex. The perturbations are mainly restricted to the sugar and phosphodiester backbone. The ribose and 3' downstream deoxyriboses are predominately in N-type conformation, while backbone torsion angles epsilon and/or zeta of the ribonucleotide or upstream deoxyribonucleotide are affected. Depending on the flanking sequences, the C2'-OH group forms hydrogen bonds with the backbone, 3'- neighboring base and/or sugar. Interestingly, even in a similar purine-rG-pyrimidine environment (A-rG-C and G-rG-C), a riboguanosine affects DNA in a distinct manner and manifests different hydrogen bonds, which makes generalizations difficult.

-	~~Authors:~~ Evich, M., Spring-Connell~~, A.M.~~, Storici, F., Germann~~, M~~.W.	+	Structural impact of single ribonucleotides in DNA.,Evich M, Spring-Connell AM, Storici F, Germann MW Chembiochem. 2016 Aug 9. doi: 10.1002/cbic.201600385. PMID:27504600<ref>PMID:27504600</ref>

-	~~Description: Structural impact~~ of ~~single ribonucleotides in DNA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Germann, M.W]]~~	+	<div class="pdbe-citations 5kie" style="background-color:#fffaf0;"></div>
-	~~[[Category: Spring-Connell, A.M]]~~	+	== References ==
-	~~[[Category: Storici, F]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Evich, M]]		[[Category: Evich, M]]
		+	[[Category: Germann, M W]]
		+	[[Category: Spring-Connell, A M]]
		+	[[Category: Storici, F]]
		+	[[Category: Dna]]
		+	[[Category: Ribonucleotide]]
		+	[[Category: Rna]]

OCA: Protected "5kie" [edit=sysop:move=sysop]

OCA — Thu, 23 Jun 2016 21:40:17 GMT

Protected "5kie" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:40, 23 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kie is ON HOLD Authors: Evich, M., Spring-Connell, A.M., Storici, F., Germann, M.W. Description: Structural impact of single ribonucleotides in DN...

OCA — Thu, 23 Jun 2016 21:40:16 GMT

New page: '''Unreleased structure''' The entry 5kie is ON HOLD Authors: Evich, M., Spring-Connell, A.M., Storici, F., Germann, M.W. Description: Structural impact of single ribonucleotides in DN...

New page

'''Unreleased structure'''

The entry 5kie is ON HOLD

Authors: Evich, M., Spring-Connell, A.M., Storici, F., Germann, M.W.

Description: Structural impact of single ribonucleotides in DNA
[[Category: Unreleased Structures]]
[[Category: Germann, M.W]]
[[Category: Spring-Connell, A.M]]
[[Category: Storici, F]]
[[Category: Evich, M]]