5eaq - Revision history

OCA at 06:19, 5 July 2023

2023-07-05T06:19:37Z

←Older revision		Revision as of 06:19, 5 July 2023
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	<StructureSection load='5eaq' size='340' side='right'caption='[[5eaq]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='5eaq' size='340' side='right'caption='[[5eaq]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5eaq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EAQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5EAQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5eaq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EAQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 3.201Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVC:[(1~{R},5~{R},6~{R},8~{R})-6-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-3,3-BIS(OXIDANYL)-2,4,7-TRIOXA-3$L^{4}-VANADABICYCLO[3.3.0]OCTAN-8-YL]METHYL+DIHYDROGEN+PHOSPHATE'>CVC</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CVC:[(1~{R},5~{R},6~{R},8~{R})-6-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-3,3-BIS(OXIDANYL)-2,4,7-TRIOXA-3$L^{4}-VANADABICYCLO[3.3.0]OCTAN-8-YL]METHYL+DIHYDROGEN+PHOSPHATE'>CVC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5eao\|5eao]]~~</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=5eaq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eaq OCA], [https://pdbe.org/5eaq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5eaq RCSB], [https://www.ebi.ac.uk/pdbsum/5eaq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5eaq 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=5eaq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eaq OCA], [~~http~~://pdbe.org/5eaq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5eaq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5eaq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5eaq ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
-	*[[Ribozyme\|Ribozyme]]	+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Golden, B L~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Mir, A~~]]	+	[[Category: Golden BL]]
-	[[Category: ~~Hammerhead]]~~	+	[[Category: Mir A]]
-	~~[[Category: Ribozyme]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 06:50, 22 April 2020

2020-04-22T06:50:59Z

←Older revision		Revision as of 06:50, 22 April 2020
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	==Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+==		==Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+==
-	<StructureSection load='5eaq' size='340' side='right' caption='[[5eaq]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='5eaq' size='340' side='right'caption='[[5eaq]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5eaq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EAQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5EAQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5eaq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EAQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EAQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVC:[(1~{R},5~{R},6~{R},8~{R})-6-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-3,3-BIS(OXIDANYL)-2,4,7-TRIOXA-3$L^{4}-VANADABICYCLO[3.3.0]OCTAN-8-YL]METHYL+DIHYDROGEN+PHOSPHATE'>CVC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVC:[(1~{R},5~{R},6~{R},8~{R})-6-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-3,3-BIS(OXIDANYL)-2,4,7-TRIOXA-3$L^{4}-VANADABICYCLO[3.3.0]OCTAN-8-YL]METHYL+DIHYDROGEN+PHOSPHATE'>CVC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5eao\|5eao]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5eao\|5eao]]</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=5eaq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eaq OCA], [http://pdbe.org/5eaq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eaq RCSB], [http://www.ebi.ac.uk/pdbsum/5eaq PDBsum]</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=5eaq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eaq OCA], [http://pdbe.org/5eaq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eaq RCSB], [http://www.ebi.ac.uk/pdbsum/5eaq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5eaq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5eaq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5eaq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Golden, B L]]		[[Category: Golden, B L]]
	[[Category: Mir, A]]		[[Category: Mir, A]]

OCA at 18:09, 26 February 2016

2016-02-26T18:09:17Z

←Older revision		Revision as of 18:09, 26 February 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5eaq is ~~ON HOLD until Paper~~ Publication	+	==Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+==
		+	<StructureSection load='5eaq' size='340' side='right' caption='[[5eaq]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5eaq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EAQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CVC:[(1~{R},5~{R},6~{R},8~{R})-6-(4-AZANYL-2-OXIDANYLIDENE-PYRIMIDIN-1-YL)-3,3-BIS(OXIDANYL)-2,4,7-TRIOXA-3$L^{4}-VANADABICYCLO[3.3.0]OCTAN-8-YL]METHYL+DIHYDROGEN+PHOSPHATE'>CVC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5eao\|5eao]]</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=5eaq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5eaq OCA], [http://pdbe.org/5eaq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5eaq RCSB], [http://www.ebi.ac.uk/pdbsum/5eaq PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.

-	~~Authors: Mir~~, A., Golden~~, B~~.L.	+	Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue.,Mir A, Golden BL Biochemistry. 2016 Feb 2;55(4):633-6. doi: 10.1021/acs.biochem.5b01139. Epub 2016, Jan 19. PMID:26551631<ref>PMID:26551631</ref>

-	~~Description: Two active site divalent ion in the crystal structure~~ of the ~~hammerhead ribozyme bound to a transition state analog~~-~~Mn2+~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5eaq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Golden, B L]]
	[[Category: Mir, A]]		[[Category: Mir, A]]
-	[[Category: ~~Golden, B.L~~]]	+	[[Category: Hammerhead]]
		+	[[Category: Ribozyme]]
		+	[[Category: Rna]]

OCA at 11:46, 16 December 2015

2015-12-16T11:46:04Z

←Older revision		Revision as of 11:46, 16 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5eaq is ON HOLD	+	The entry 5eaq is ON HOLD until Paper Publication

	Authors: Mir, A., Golden, B.L.		Authors: Mir, A., Golden, B.L.

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

2015-12-01T02:34:52Z

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

←Older revision

Revision as of 02:34, 1 December 2015

OCA: New page: '''Unreleased structure''' The entry 5eaq is ON HOLD Authors: Mir, A., Golden, B.L. Description: Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound ...

2015-12-01T02:34:50Z

New page: '''Unreleased structure''' The entry 5eaq is ON HOLD Authors: Mir, A., Golden, B.L. Description: Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound ...

New page

'''Unreleased structure'''

The entry 5eaq is ON HOLD

Authors: Mir, A., Golden, B.L.

Description: Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mn2+
[[Category: Unreleased Structures]]
[[Category: Mir, A]]
[[Category: Golden, B.L]]