4nlf - Revision history

OCA at 16:58, 20 September 2023

OCA — Wed, 20 Sep 2023 16:58:57 GMT

←Older revision		Revision as of 16:58, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nlf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NLF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nlf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NLF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FC:2-TRIFLUOROMETHYLTHIO-2-DEOXYCYTIDINE'>6FC</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6FC:2-TRIFLUOROMETHYLTHIO-2-DEOXYCYTIDINE'>6FC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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;~~'>~~[[3dvz\|3dvz]], [[1q9a\|1q9a]], [[3dw4\|3dw4]], [[3dw5\|3dw5]], [[3dw6\|3dw6]], [[3dw7\|3dw7]], [[4nmg\|4nmg]], [[4nxh\|4nxh]]~~</~~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=4nlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nlf OCA], [https://pdbe.org/4nlf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nlf RCSB], [https://www.ebi.ac.uk/pdbsum/4nlf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nlf 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=4nlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nlf OCA], [https://pdbe.org/4nlf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nlf RCSB], [https://www.ebi.ac.uk/pdbsum/4nlf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nlf ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ennifar, E]]	+	[[Category: Ennifar E]]
-	[[Category: Kosutic, M]]	+	[[Category: Kosutic M]]
-	[[Category: Micura, R]]	+	[[Category: Micura R]]
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna hairpin]]~~	+
-	~~[[Category: Structural~~]]	+

OCA at 05:13, 15 June 2022

OCA — Wed, 15 Jun 2022 05:13:36 GMT

←Older revision		Revision as of 05:13, 15 June 2022
Line 3:		Line 3:
	<StructureSection load='4nlf' size='340' side='right'caption='[[4nlf]], [[Resolution\|resolution]] 1.00Å' scene=''>		<StructureSection load='4nlf' size='340' side='right'caption='[[4nlf]], [[Resolution\|resolution]] 1.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nlf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NLF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NLF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nlf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NLF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NLF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FC:2-TRIFLUOROMETHYLTHIO-2-DEOXYCYTIDINE'>6FC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FC:2-TRIFLUOROMETHYLTHIO-2-DEOXYCYTIDINE'>6FC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dvz\|3dvz]], [[1q9a\|1q9a]], [[3dw4\|3dw4]], [[3dw5\|3dw5]], [[3dw6\|3dw6]], [[3dw7\|3dw7]], [[4nmg\|4nmg]], [[4nxh\|4nxh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3dvz\|3dvz]], [[1q9a\|1q9a]], [[3dw4\|3dw4]], [[3dw5\|3dw5]], [[3dw6\|3dw6]], [[3dw7\|3dw7]], [[4nmg\|4nmg]], [[4nxh\|4nxh]]</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=4nlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nlf OCA], [~~http~~://pdbe.org/4nlf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nlf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nlf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nlf 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=4nlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nlf OCA], [https://pdbe.org/4nlf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nlf RCSB], [https://www.ebi.ac.uk/pdbsum/4nlf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nlf ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The chemical synthesis of ribonucleic acids (RNA) with novel chemical modifications is largely driven by the motivation to identify eligible functional probes for the various applications in life sciences. To this end, we have a strong focus on the development of novel fluorinated RNA derivatives that are powerful in NMR spectroscopic analysis of RNA folding and RNA ligand interactions. Here, we report on the synthesis of 2'-SCF3 pyrimidine nucleoside containing oligoribonucleotides and the comprehensive investigation of their structure and base pairing properties. While this modification has a modest impact on thermodynamic stability when it resides in single-stranded regions, it was found to be destabilizing to a surprisingly high extent when located in double helical regions. Our NMR spectroscopic investigations on short single-stranded RNA revealed a strong preference for C2'-endo conformation of the 2'-SCF3 ribose unit. Together with a recent computational study (L. Li, J. W. Szostak, J. Am. Chem. Soc. 2014, 136, 2858-2865) that estimated the extent of destabilization caused by a single C2'-endo nucleotide within a native RNA duplex to amount to 6 kcal mol(-1) because of disruption of the planar base pair structure, these findings support the notion that the intrinsic preference for C2'-endo conformation of 2'-SCF3 nucleosides is most likely responsible for the pronounced destabilization of double helices. Importantly, we were able to crystallize 2'-SCF3 modified RNAs and solved their X-ray structures at atomic resolution. Interestingly, the 2'-SCF3 containing nucleosides that were engaged in distinct mismatch arrangements, but also in a standard Watson-Crick base pair, adopted the same C3'-endo ribose conformations as observed in the structure of the unmodified RNA. Likely, strong crystal packing interactions account for this observation. In all structures, the fluorine atoms made surprisingly close contacts to the oxygen atoms of the corresponding pyrimidine nucleobase (O2), and the 2'-SCF3 moieties participated in defined water-bridged hydrogen-bonding networks in the minor groove. All these features allow a rationalization of the structural determinants of the 2'-SCF3 nucleoside modification and correlate them to base pairing properties.
		+
		+	Surprising base pairing and structural properties of 2'-trifluoromethylthio-modified ribonucleic acids.,Kosutic M, Jud L, Da Veiga C, Frener M, Fauster K, Kreutz C, Ennifar E, Micura R J Am Chem Soc. 2014 May 7;136(18):6656-63. doi: 10.1021/ja5005637. Epub 2014 Apr , 25. PMID:24766131<ref>PMID:24766131</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4nlf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:55, 10 April 2019

OCA — Wed, 10 Apr 2019 08:55:56 GMT

←Older revision		Revision as of 08:55, 10 April 2019
Line 1:		Line 1:

	==2'-trifluoromethylthio-2'-deoxycytidine-modified SRL==		==2'-trifluoromethylthio-2'-deoxycytidine-modified SRL==
-	<StructureSection load='4nlf' size='340' side='right' caption='[[4nlf]], [[Resolution\|resolution]] 1.00Å' scene=''>	+	<StructureSection load='4nlf' size='340' side='right'caption='[[4nlf]], [[Resolution\|resolution]] 1.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nlf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NLF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NLF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nlf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NLF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NLF FirstGlance]. <br>
Line 11:		Line 11:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ennifar, E]]		[[Category: Ennifar, E]]
	[[Category: Kosutic, M]]		[[Category: Kosutic, M]]

OCA at 20:17, 11 August 2016

OCA — Thu, 11 Aug 2016 20:17:29 GMT

←Older revision		Revision as of 20:17, 11 August 2016
Line 1:		Line 1:
		+
	==2'-trifluoromethylthio-2'-deoxycytidine-modified SRL==		==2'-trifluoromethylthio-2'-deoxycytidine-modified SRL==
	<StructureSection load='4nlf' size='340' side='right' caption='[[4nlf]], [[Resolution\|resolution]] 1.00Å' scene=''>		<StructureSection load='4nlf' size='340' side='right' caption='[[4nlf]], [[Resolution\|resolution]] 1.00Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FC:2-TRIFLUOROMETHYLTHIO-2-DEOXYCYTIDINE'>6FC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FC:2-TRIFLUOROMETHYLTHIO-2-DEOXYCYTIDINE'>6FC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dvz\|3dvz]], [[1q9a\|1q9a]], [[3dw4\|3dw4]], [[3dw5\|3dw5]], [[3dw6\|3dw6]], [[3dw7\|3dw7]], [[4nmg\|4nmg]], [[4nxh\|4nxh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dvz\|3dvz]], [[1q9a\|1q9a]], [[3dw4\|3dw4]], [[3dw5\|3dw5]], [[3dw6\|3dw6]], [[3dw7\|3dw7]], [[4nmg\|4nmg]], [[4nxh\|4nxh]]</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=4nlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nlf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nlf RCSB], [http://www.ebi.ac.uk/pdbsum/4nlf 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=4nlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nlf OCA], [http://pdbe.org/4nlf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nlf RCSB], [http://www.ebi.ac.uk/pdbsum/4nlf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nlf ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 12:50, 19 November 2014

OCA — Wed, 19 Nov 2014 12:50:43 GMT

←Older revision		Revision as of 12:50, 19 November 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==2'-trifluoromethylthio-2'-deoxycytidine-modified SRL==
-		+	<StructureSection load='4nlf' size='340' side='right' caption='[[4nlf]], [[Resolution\|resolution]] 1.00Å' scene=''>
-	~~The entry~~ 4nlf is ~~ON HOLD until Nov 19 2015~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4nlf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NLF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NLF FirstGlance]. <br>
-	~~Authors~~: ~~Ennifar~~, E., ~~Micura~~, R., Kosutic, M.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6FC:2-TRIFLUOROMETHYLTHIO-2-DEOXYCYTIDINE'>6FC</scene></td></tr>
-	~~Description~~: ~~2'-trifluoromethylthio-2'-deoxycytidine-modified SRL~~	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3dvz\|3dvz]], [[1q9a\|1q9a]], [[3dw4\|3dw4]], [[3dw5\|3dw5]], [[3dw6\|3dw6]], [[3dw7\|3dw7]], [[4nmg\|4nmg]], [[4nxh\|4nxh]]</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=4nlf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nlf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nlf RCSB], [http://www.ebi.ac.uk/pdbsum/4nlf PDBsum]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ennifar, E]]
		+	[[Category: Kosutic, M]]
		+	[[Category: Micura, R]]
		+	[[Category: Rna]]
		+	[[Category: Rna hairpin]]
		+	[[Category: Structural]]

OCA at 22:50, 1 October 2014

OCA — Wed, 01 Oct 2014 22:50:15 GMT

←Older revision		Revision as of 22:50, 1 October 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4nlf is ON HOLD until ~~Paper Publication~~	+	The entry 4nlf is ON HOLD until Nov 19 2015

	Authors: Ennifar, E., Micura, R., Kosutic, M.		Authors: Ennifar, E., Micura, R., Kosutic, M.

	Description: 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL		Description: 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL

OCA at 10:17, 5 February 2014

OCA — Wed, 05 Feb 2014 10:17:54 GMT

←Older revision		Revision as of 10:17, 5 February 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4nlf is ON HOLD	+	The entry 4nlf is ON HOLD until Paper Publication

	Authors: Ennifar, E., Micura, R., Kosutic, M.		Authors: Ennifar, E., Micura, R., Kosutic, M.

	Description: 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL		Description: 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL

OCA at 09:50, 27 November 2013

OCA — Wed, 27 Nov 2013 09:50:22 GMT

←Older revision		Revision as of 09:50, 27 November 2013
Line 5:		Line 5:
	Authors: Ennifar, E., Micura, R., Kosutic, M.		Authors: Ennifar, E., Micura, R., Kosutic, M.

-	Description: 2'-trifluoromethylthio-2'-~~deoxy cytidine~~-modified SRL	+	Description: 2'-trifluoromethylthio-2'-deoxycytidine-modified SRL

OCA: Protected "4nlf" [edit=sysop:move=sysop]

OCA — Wed, 20 Nov 2013 13:02:04 GMT

Protected "4nlf" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:02, 20 November 2013

OCA: New page: '''Unreleased structure''' The entry 4nlf is ON HOLD Authors: Ennifar, E., Micura, R., Kosutic, M. Description: 2'-trifluoromethylthio-2'-deoxy cytidine-modified SRL

OCA — Wed, 20 Nov 2013 13:02:03 GMT

New page: '''Unreleased structure''' The entry 4nlf is ON HOLD Authors: Ennifar, E., Micura, R., Kosutic, M. Description: 2'-trifluoromethylthio-2'-deoxy cytidine-modified SRL

New page

'''Unreleased structure'''

The entry 4nlf is ON HOLD

Authors: Ennifar, E., Micura, R., Kosutic, M.

Description: 2'-trifluoromethylthio-2'-deoxy cytidine-modified SRL