4h0b - Revision history

OCA at 11:35, 1 March 2024

2024-03-01T11:35:17Z

←Older revision		Revision as of 11:35, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4h0b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ock 3ock]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H0B FirstGlance]. <br>		<table><tr><td colspan='2'>[[4h0b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ock 3ock]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H0B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <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]] 1.26Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4h0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h0b OCA], [https://pdbe.org/4h0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h0b RCSB], [https://www.ebi.ac.uk/pdbsum/4h0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h0b 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=4h0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h0b OCA], [https://pdbe.org/4h0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h0b RCSB], [https://www.ebi.ac.uk/pdbsum/4h0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h0b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.		[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Sperm whale myoglobin (Mb) has weak dehaloperoxidase activity and catalyzes the peroxidative dehalogenation of 2,4,6-trichlorophenol (TCP) to 2,6-dichloroquinone. Crystals of Mb and of its more active G65T variant were used to study the binding of TCP, 4-iodophenol (4-IP) and phenol. The structures of crystals soaked overnight in a 10 mM solution of phenol revealed that a phenol molecule binds in the proximal cavity, forming a hydrogen bond to the hydroxyl of Tyr146 and hydrophobic contacts which include interactions with C(beta) and C(gamma) of the proximal histidine His93. The phenol position corresponds to the strongest xenon binding site, Xe1. It appears that the ligand enters the proximal cavity through a gate formed by the flexible loops 79-86 and 93-103. TCP and 4-IP do not bind to Mb in this manner under similar conditions; however, it appears to be likely that dimethyl sulfoxide (DMSO), which was used at a concentration of 0.8 M to facilitate 4-IP dissolution, binds in the phenol/Xe1 binding site. In this structure, a water molecule coordinated to the heme iron was replaced by an oxygen molecule, reflecting the reduction of the heme. Crystals of Mb and G65T Mb soaked for 5-10 min did not show bound phenol. Kinetic studies of TCP dechlorination showed that phenol has a dual effect: it acts as a competitive inhibitor that is likely to interfere with TCP binding at the heme edge and as a weak activator, likely through binding in the proximal cavity. The lack of phenol bound at the heme edge in the crystal structures suggests that its inhibitory binding only takes place when the heme is activated by hydrogen peroxide.
-
-	Complex of myoglobin with phenol bound in a proximal cavity.,Huang X, Wang C, Celeste LR, Lovelace LL, Sun S, Dawson JH, Lebioda L Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 1;68(Pt 12):1465-71., doi: 10.1107/S1744309112045514. Epub 2012 Nov 19. PMID:23192025<ref>PMID:23192025</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4h0b" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Myoglobin 3D structures\|Myoglobin 3D structures]]		*[[Myoglobin 3D structures\|Myoglobin 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:51, 3 November 2022

2022-11-03T07:51:32Z

←Older revision		Revision as of 07:51, 3 November 2022
Line 1:		Line 1:

	==Complex of G65T Myoglobin with DMSO in its Distal Cavity==		==Complex of G65T Myoglobin with DMSO in its Distal Cavity==
-	<StructureSection load='4h0b' size='340' side='right' caption='[[4h0b]], [[Resolution\|resolution]] 1.26Å' scene=''>	+	<StructureSection load='4h0b' size='340' side='right'caption='[[4h0b]], [[Resolution\|resolution]] 1.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h0b]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Phycd Phycd~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ock 3ock]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H0B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4H0B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h0b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ock 3ock]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H0B FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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">[[4h07\|4h07]]</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=4h0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h0b OCA], [https://pdbe.org/4h0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h0b RCSB], [https://www.ebi.ac.uk/pdbsum/4h0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h0b ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9755 PHYCD])~~</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=4h0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h0b OCA], [~~http~~://pdbe.org/4h0b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4h0b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4h0b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4h0b ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.	+	[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4h0b" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4h0b" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Myoglobin 3D structures\|Myoglobin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Phycd~~]]	+	[[Category: Large Structures]]
-	[[Category: Celeste~~, L R~~]]	+	[[Category: Physeter catodon]]
-	[[Category: Dawson~~, J H~~]]	+	[[Category: Celeste LR]]
-	[[Category: Huang, X]]	+	[[Category: Dawson JH]]
-	[[Category: Lebioda, L]]	+	[[Category: Huang X]]
-	[[Category: Lovelace~~, L L~~]]	+	[[Category: Lebioda L]]
-	[[Category: Shengfang, S]]	+	[[Category: Lovelace LL]]
-	[[Category: Wang, C]]	+	[[Category: Shengfang S]]
-	~~[[Category: Oxygen transport~~]]	+	[[Category: Wang C]]

OCA at 08:34, 15 November 2017

2017-11-15T08:34:45Z

←Older revision		Revision as of 08:34, 15 November 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4h0b" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4h0b" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Myoglobin\|Myoglobin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:18, 5 August 2016

2016-08-05T19:18:53Z

←Older revision		Revision as of 19:18, 5 August 2016
Line 1:		Line 1:
		+
	==Complex of G65T Myoglobin with DMSO in its Distal Cavity==		==Complex of G65T Myoglobin with DMSO in its Distal Cavity==
	<StructureSection load='4h0b' size='340' side='right' caption='[[4h0b]], [[Resolution\|resolution]] 1.26Å' scene=''>		<StructureSection load='4h0b' size='340' side='right' caption='[[4h0b]], [[Resolution\|resolution]] 1.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h0b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Physeter_catodon Physeter catodon~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ock 3ock]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H0B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h0b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Phycd Phycd]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ock 3ock]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H0B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <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"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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">[[4h07\|4h07]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4h07\|4h07]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9755 ~~Physeter catodon~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9755 PHYCD])</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=4h0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h0b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h0b RCSB], [http://www.ebi.ac.uk/pdbsum/4h0b 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=4h0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h0b OCA], [http://pdbe.org/4h0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h0b RCSB], [http://www.ebi.ac.uk/pdbsum/4h0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h0b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4h0b" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Physeter catodon~~]]	+	[[Category: Phycd]]
	[[Category: Celeste, L R]]		[[Category: Celeste, L R]]
	[[Category: Dawson, J H]]		[[Category: Dawson, J H]]

OCA at 21:15, 25 December 2014

2014-12-25T21:15:44Z

←Older revision		Revision as of 21:15, 25 December 2014
Line 8:		Line 8:
	<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=4h0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h0b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h0b RCSB], [http://www.ebi.ac.uk/pdbsum/4h0b 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=4h0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h0b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h0b RCSB], [http://www.ebi.ac.uk/pdbsum/4h0b PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 09:41, 10 December 2014

2014-12-10T09:41:25Z

←Older revision		Revision as of 09:41, 10 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4h0b.~~png~~\|~~left~~\|~~200px~~]]	+	==Complex of G65T Myoglobin with DMSO in its Distal Cavity==
		+	<StructureSection load='4h0b' size='340' side='right' caption='[[4h0b]], [[Resolution\|resolution]] 1.26Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4h0b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ock 3ock]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H0B FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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">[[4h07\|4h07]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9755 Physeter catodon])</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=4h0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h0b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h0b RCSB], [http://www.ebi.ac.uk/pdbsum/4h0b PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Sperm whale myoglobin (Mb) has weak dehaloperoxidase activity and catalyzes the peroxidative dehalogenation of 2,4,6-trichlorophenol (TCP) to 2,6-dichloroquinone. Crystals of Mb and of its more active G65T variant were used to study the binding of TCP, 4-iodophenol (4-IP) and phenol. The structures of crystals soaked overnight in a 10 mM solution of phenol revealed that a phenol molecule binds in the proximal cavity, forming a hydrogen bond to the hydroxyl of Tyr146 and hydrophobic contacts which include interactions with C(beta) and C(gamma) of the proximal histidine His93. The phenol position corresponds to the strongest xenon binding site, Xe1. It appears that the ligand enters the proximal cavity through a gate formed by the flexible loops 79-86 and 93-103. TCP and 4-IP do not bind to Mb in this manner under similar conditions; however, it appears to be likely that dimethyl sulfoxide (DMSO), which was used at a concentration of 0.8 M to facilitate 4-IP dissolution, binds in the phenol/Xe1 binding site. In this structure, a water molecule coordinated to the heme iron was replaced by an oxygen molecule, reflecting the reduction of the heme. Crystals of Mb and G65T Mb soaked for 5-10 min did not show bound phenol. Kinetic studies of TCP dechlorination showed that phenol has a dual effect: it acts as a competitive inhibitor that is likely to interfere with TCP binding at the heme edge and as a weak activator, likely through binding in the proximal cavity. The lack of phenol bound at the heme edge in the crystal structures suggests that its inhibitory binding only takes place when the heme is activated by hydrogen peroxide.

-	~~{{STRUCTURE_4h0b\| PDB=4h0b \| SCENE= }}~~	+	Complex of myoglobin with phenol bound in a proximal cavity.,Huang X, Wang C, Celeste LR, Lovelace LL, Sun S, Dawson JH, Lebioda L Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Dec 1;68(Pt 12):1465-71., doi: 10.1107/S1744309112045514. Epub 2012 Nov 19. PMID:23192025<ref>PMID:23192025</ref>

-	~~===Complex~~ of ~~G65T Myoglobin with DMSO in its Distal Cavity===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_23192025}}~~	+	==See Also==
-		+	*[[Myoglobin\|Myoglobin]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~4h0b~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=~~1&id~~=~~3ock 3ock]. Full crystallographic information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=4H0B OCA].~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Physeter catodon]]		[[Category: Physeter catodon]]
-	[[Category: Celeste, L R.]]	+	[[Category: Celeste, L R]]
-	[[Category: Dawson, J H.]]	+	[[Category: Dawson, J H]]
-	[[Category: Huang, X.]]	+	[[Category: Huang, X]]
-	[[Category: Lebioda, L.]]	+	[[Category: Lebioda, L]]
-	[[Category: Lovelace, L L.]]	+	[[Category: Lovelace, L L]]
-	[[Category: Shengfang, S.]]	+	[[Category: Shengfang, S]]
-	[[Category: Wang, C.]]	+	[[Category: Wang, C]]
	[[Category: Oxygen transport]]		[[Category: Oxygen transport]]

OCA at 21:11, 12 December 2012

2012-12-12T21:11:25Z

←Older revision		Revision as of 21:11, 12 December 2012
Line 1:		Line 1:
-	[[Image:4h0b.~~jpg~~\|left\|200px]]	+	[[Image:4h0b.png\|left\|200px]]

	{{STRUCTURE_4h0b\| PDB=4h0b \| SCENE= }}		{{STRUCTURE_4h0b\| PDB=4h0b \| SCENE= }}
Line 5:		Line 5:
	===Complex of G65T Myoglobin with DMSO in its Distal Cavity===		===Complex of G65T Myoglobin with DMSO in its Distal Cavity===

		+	{{ABSTRACT_PUBMED_23192025}}

	==About this Structure==		==About this Structure==

OCA at 09:24, 21 November 2012

2012-11-21T09:24:41Z

←Older revision		Revision as of 09:24, 21 November 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4h0b.jpg\|left\|200px]]

-	~~The entry~~ 4h0b ~~is ON HOLD~~	+	{{STRUCTURE_4h0b\| PDB=4h0b \| SCENE= }}

-	~~Authors: Lebioda, L., Lovelace, L.L., Celeste, L.R., Huang, X., Wang, C., Shengfang, S., Dawson, J.H.~~	+	===Complex of G65T Myoglobin with DMSO in its Distal Cavity===

-	~~Description: Complex of G65T Myoglobin~~ with ~~DMSO in its Distal Cavity~~	+
		+	==About this Structure==
		+	[[4h0b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3ock 3ock]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H0B OCA].
		+	[[Category: Physeter catodon]]
		+	[[Category: Celeste, L R.]]
		+	[[Category: Dawson, J H.]]
		+	[[Category: Huang, X.]]
		+	[[Category: Lebioda, L.]]
		+	[[Category: Lovelace, L L.]]
		+	[[Category: Shengfang, S.]]
		+	[[Category: Wang, C.]]
		+	[[Category: Oxygen transport]]

OCA at 05:46, 3 October 2012

2012-10-03T05:46:18Z

←Older revision		Revision as of 05:46, 3 October 2012
Line 3:		Line 3:
	The entry 4h0b is ON HOLD		The entry 4h0b is ON HOLD

-	Authors: Lebioda, L., Lovelace, L.L., Celeste, L.R., Huang, X., Wang, C, Shengfang,S., Dawson, J,H..	+	Authors: Lebioda, L., Lovelace, L.L., Celeste, L.R., Huang, X., Wang, C., Shengfang, S., Dawson, J.H.

	Description: Complex of G65T Myoglobin with DMSO in its Distal Cavity		Description: Complex of G65T Myoglobin with DMSO in its Distal Cavity

OCA: Protected "4h0b" [edit=sysop:move=sysop]

2012-09-19T06:56:24Z

Protected "4h0b" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:56, 19 September 2012