5yz2 - Revision history

OCA at 08:41, 22 November 2023

OCA — Wed, 22 Nov 2023 08:41:08 GMT

←Older revision		Revision as of 08:41, 22 November 2023
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	<StructureSection load='5yz2' size='340' side='right'caption='[[5yz2]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5yz2' size='340' side='right'caption='[[5yz2]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yz2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YZ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yz2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZ2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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]] 1.75Å</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=5yz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz2 OCA], [~~http~~://pdbe.org/5yz2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yz2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yz2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz2 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=5yz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz2 OCA], [https://pdbe.org/5yz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yz2 RCSB], [https://www.ebi.ac.uk/pdbsum/5yz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CORC_ECOLI CORC_ECOLI]] Plays a role in the transport of magnesium and cobalt ions.	+	[https://www.uniprot.org/uniprot/CORC_ECOLI CORC_ECOLI] Plays a role in the transport of magnesium and cobalt ions.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Feng, N]]	+	[[Category: Feng N]]
-	[[Category: Li~~, D F~~]]	+	[[Category: Li DF]]
-	[[Category: Qi, C]]	+	[[Category: Qi C]]
-	[[Category: Wang~~, D C]]~~	+	[[Category: Wang DC]]
-	~~[[Category: Amp binding]]~~	+
-	~~[[Category: Magnesium and cobalt efflux protein]]~~	+
-	~~[[Category: Metal transport~~]]	+

OCA at 09:31, 21 October 2020

OCA — Wed, 21 Oct 2020 09:31:44 GMT

←Older revision		Revision as of 09:31, 21 October 2020
Line 1:		Line 1:

	==the cystathionine-beta-synthase (CBS) domain of magnesium and cobalt efflux protein CorC in complex with both C2'- and C3'-endo AMP==		==the cystathionine-beta-synthase (CBS) domain of magnesium and cobalt efflux protein CorC in complex with both C2'- and C3'-endo AMP==
-	<StructureSection load='5yz2' size='340' side='right' caption='[[5yz2]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5yz2' size='340' side='right'caption='[[5yz2]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yz2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YZ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yz2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YZ2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=5yz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz2 OCA], [http://pdbe.org/5yz2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yz2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yz2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz2 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=5yz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz2 OCA], [http://pdbe.org/5yz2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yz2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yz2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Feng, N]]		[[Category: Feng, N]]
	[[Category: Li, D F]]		[[Category: Li, D F]]

OCA at 05:29, 30 May 2018

OCA — Wed, 30 May 2018 05:29:22 GMT

←Older revision		Revision as of 05:29, 30 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yz2 is ~~ON HOLD until Paper~~ Publication	+	==the cystathionine-beta-synthase (CBS) domain of magnesium and cobalt efflux protein CorC in complex with both C2'- and C3'-endo AMP==
		+	<StructureSection load='5yz2' size='340' side='right' caption='[[5yz2]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yz2]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZ2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=5yz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yz2 OCA], [http://pdbe.org/5yz2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yz2 RCSB], [http://www.ebi.ac.uk/pdbsum/5yz2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yz2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CORC_ECOLI CORC_ECOLI]] Plays a role in the transport of magnesium and cobalt ions.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The equilibrium between C2'- and C3'-endo conformations of nucleotides in solution, as well as their polymers DNA and RNA, has been well studied in previous work. However, this equilibrium of nucleotides in their binding state remains unclear. We observed two AMP molecules, in C3'- and C2'-endo conformations respectively, simultaneously bound to a cystathionine-beta-synthase (CBS) domain dimer of the magnesium and cobalt efflux protein CorC in the crystallographic study. The C2'-endo AMP molecule assumes the higher sugar pucker energy and one more hydrogen bond with the protein than the C3'-endo molecule does. The balance between the high sugar pucker energy and the low binding energy suggests an equilibrium or switch between C2'- and C3'-endo conformations of the bound nucleotides. Our work challenge the previous hypothesis that the ribose of the bound nucleotides would be locked in a fixed conformation.

-	~~Authors: Feng~~, N., Qi, C., Li, ~~D.F.~~, Wang, D.C.	+	The C2'- and C3'-endo equilibrium for AMP molecules bound in the cystathionine-beta-synthase domain.,Feng N, Qi C, Hou YJ, Zhang Y, Wang DC, Li DF Biochem Biophys Res Commun. 2018 Mar 4;497(2):646-651. doi:, 10.1016/j.bbrc.2018.02.124. Epub 2018 Feb 15. PMID:29453981<ref>PMID:29453981</ref>

-	~~Description:~~ the ~~cystathionine-beta-synthase (CBS) domain~~ of ~~magnesium and cobalt efflux protein CorC in complex with both C2'~~-~~and C3'~~-~~endo AMP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Li, D.F]]~~	+	<div class="pdbe-citations 5yz2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Feng, N]]		[[Category: Feng, N]]
		+	[[Category: Li, D F]]
	[[Category: Qi, C]]		[[Category: Qi, C]]
-	[[Category: Wang, D.C]]	+	[[Category: Wang, D C]]
		+	[[Category: Amp binding]]
		+	[[Category: Magnesium and cobalt efflux protein]]
		+	[[Category: Metal transport]]

OCA at 04:50, 3 January 2018

OCA — Wed, 03 Jan 2018 04:50:33 GMT

←Older revision		Revision as of 04:50, 3 January 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yz2 is ON HOLD	+	The entry 5yz2 is ON HOLD until Paper Publication

	Authors: Feng, N., Qi, C., Li, D.F., Wang, D.C.		Authors: Feng, N., Qi, C., Li, D.F., Wang, D.C.

OCA: Protected "5yz2" [edit=sysop:move=sysop]

OCA — Wed, 20 Dec 2017 04:52:32 GMT

Protected "5yz2" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:52, 20 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yz2 is ON HOLD Authors: Feng, N., Qi, C., Li, D.F., Wang, D.C. Description: the cystathionine-beta-synthase (CBS) domain of magnesium and cobalt e...

OCA — Wed, 20 Dec 2017 04:52:31 GMT

New page: '''Unreleased structure''' The entry 5yz2 is ON HOLD Authors: Feng, N., Qi, C., Li, D.F., Wang, D.C. Description: the cystathionine-beta-synthase (CBS) domain of magnesium and cobalt e...

New page

'''Unreleased structure'''

The entry 5yz2 is ON HOLD

Authors: Feng, N., Qi, C., Li, D.F., Wang, D.C.

Description: the cystathionine-beta-synthase (CBS) domain of magnesium and cobalt efflux protein CorC in complex with both C2'-and C3'-endo AMP
[[Category: Unreleased Structures]]
[[Category: Li, D.F]]
[[Category: Feng, N]]
[[Category: Qi, C]]
[[Category: Wang, D.C]]