1gza - Revision history

OCA at 11:26, 27 March 2024

OCA — Wed, 27 Mar 2024 11:26:04 GMT

←Older revision		Revision as of 11:26, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='1gza' size='340' side='right'caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='1gza' size='340' side='right'caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/'~~arthromyces_ramosus~~' '~~arthromyces~~ ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GZA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agaricales_sp._'Arthromyces_ramosus' Agaricales sp. 'Arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GZA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.06Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [https://pdbe.org/1gza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [https://www.ebi.ac.uk/pdbsum/1gza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gza 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=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [https://pdbe.org/1gza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [https://www.ebi.ac.uk/pdbsum/1gza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gza ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PER_ARTRA PER_ARTRA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gza ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gza ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The site and characteristics of iodide binding to Arthromyces ramosus peroxidase were examined by x-ray crystallographic analysis, 1H and 127I NMR, and kinetic studies. X-ray analysis of an A. ramosus peroxidase crystal soaked in a KI solution at pH 5.5 showed that a single iodide ion is located at the entrance of the access channel to the distal side of the heme and lies between the two peptide segments, Phe90-Pro91-Ala92 and Ser151-Leu152-Ile153, 12.8 A from the heme iron. The distances between the iodide ion and heme peripheral methyl groups were all more than 10 A. The findings agree with the results obtained with 1H NMR in which the chemical shift and intensity of the methyl groups in the hyperfine shift region of A. ramosus peroxidase were hardly affected by the addition of iodide, unlike the case of horseradish peroxidase. Moreover, 127I NMR and steady-state kinetics showed that the binding of iodide depends on protonation of an amino acid residue with a pKa of about 5.3, which presumably is the distal histidine (His56), 7.8 A away from the iodide ion. The mechanism of electron transfer from the iodide ion to the heme iron is discussed on the basis of these findings.
-
-	Binding of iodide to Arthromyces ramosus peroxidase investigated with X-ray crystallographic analysis, 1H and 127I NMR spectroscopy, and steady-state kinetics.,Fukuyama K, Sato K, Itakura H, Takahashi S, Hosoya T J Biol Chem. 1997 Feb 28;272(9):5752-6. PMID:9038188<ref>PMID:9038188</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1gza" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arthromyces ramosus]]	+	[[Category: Agaricales sp. 'Arthromyces ramosus']]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peroxidase]]~~	+	[[Category: Fukuyama K]]
-	[[Category: Fukuyama, K]]	+	[[Category: Itakura H]]
-	[[Category: Itakura, H]]	+
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:30, 28 July 2021

OCA — Wed, 28 Jul 2021 11:30:28 GMT

←Older revision		Revision as of 11:30, 28 July 2021
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	<StructureSection load='1gza' size='340' side='right'caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='1gza' size='340' side='right'caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/'arthromyces_ramosus' 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1GZA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/'arthromyces_ramosus' 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GZA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </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=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [~~http~~://pdbe.org/1gza PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1gza PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1gza 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=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [https://pdbe.org/1gza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [https://www.ebi.ac.uk/pdbsum/1gza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gza ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:42, 23 October 2019

OCA — Wed, 23 Oct 2019 08:42:28 GMT

←Older revision		Revision as of 08:42, 23 October 2019
Line 1:		Line 1:

	==PEROXIDASE==		==PEROXIDASE==
-	<StructureSection load='1gza' size='340' side='right' caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>	+	<StructureSection load='1gza' size='340' side='right'caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'arthromyces_ramosus' 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GZA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'arthromyces_ramosus' 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GZA FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gz/1gza_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gz/1gza_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Arthromyces ramosus]]		[[Category: Arthromyces ramosus]]
		+	[[Category: Large Structures]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
	[[Category: Fukuyama, K]]		[[Category: Fukuyama, K]]

OCA at 06:36, 29 November 2017

OCA — Wed, 29 Nov 2017 06:36:57 GMT

←Older revision		Revision as of 06:36, 29 November 2017
Line 1:		Line 1:
		+
	==PEROXIDASE==		==PEROXIDASE==
	<StructureSection load='1gza' size='340' side='right' caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='1gza' size='340' side='right' caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Agaricales_sp._~~'arthromyces_ramosus' ~~Agaricales sp.~~ 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GZA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'arthromyces_ramosus' 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GZA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </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=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [http://pdbe.org/1gza PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [http://www.ebi.ac.uk/pdbsum/1gza 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=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [http://pdbe.org/1gza PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [http://www.ebi.ac.uk/pdbsum/1gza PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gza ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Agaricales sp. 'arthromyces~~ ramosus']]	+	[[Category: Arthromyces ramosus]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
	[[Category: Fukuyama, K]]		[[Category: Fukuyama, K]]

OCA at 18:41, 9 February 2016

OCA — Tue, 09 Feb 2016 18:41:30 GMT

←Older revision		Revision as of 18:41, 9 February 2016
Line 15:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gza ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:59, 11 September 2015

OCA — Fri, 11 Sep 2015 00:59:27 GMT

←Older revision		Revision as of 00:59, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1gza' size='340' side='right' caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='1gza' size='340' side='right' caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Eukaryota Eukaryota~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GZA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agaricales_sp._'arthromyces_ramosus' Agaricales sp. 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GZA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </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=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [http://www.ebi.ac.uk/pdbsum/1gza 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=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [http://pdbe.org/1gza PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [http://www.ebi.ac.uk/pdbsum/1gza PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1gza" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Eukaryota~~]]	+	[[Category: Agaricales sp. 'arthromyces ramosus']]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
	[[Category: Fukuyama, K]]		[[Category: Fukuyama, K]]

OCA at 21:09, 22 December 2014

OCA — Mon, 22 Dec 2014 21:09:46 GMT

←Older revision		Revision as of 21:09, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GZA FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GZA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [http://www.ebi.ac.uk/pdbsum/1gza 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=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [http://www.ebi.ac.uk/pdbsum/1gza PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	[[Category: Eukaryota]]		[[Category: Eukaryota]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
-	[[Category: Fukuyama, K.]]	+	[[Category: Fukuyama, K]]
-	[[Category: Itakura, H.]]	+	[[Category: Itakura, H]]
	[[Category: Glycoprotein]]		[[Category: Glycoprotein]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Peroxidase]]

OCA at 11:01, 28 September 2014

OCA — Sun, 28 Sep 2014 11:01:10 GMT

←Older revision		Revision as of 11:01, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1gza.~~png\|left~~\|200px]]	+	==PEROXIDASE==
		+	<StructureSection load='1gza' size='340' side='right' caption='[[1gza]], [[Resolution\|resolution]] 2.06Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1gza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GZA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gza OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gza RCSB], [http://www.ebi.ac.uk/pdbsum/1gza PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gz/1gza_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The site and characteristics of iodide binding to Arthromyces ramosus peroxidase were examined by x-ray crystallographic analysis, 1H and 127I NMR, and kinetic studies. X-ray analysis of an A. ramosus peroxidase crystal soaked in a KI solution at pH 5.5 showed that a single iodide ion is located at the entrance of the access channel to the distal side of the heme and lies between the two peptide segments, Phe90-Pro91-Ala92 and Ser151-Leu152-Ile153, 12.8 A from the heme iron. The distances between the iodide ion and heme peripheral methyl groups were all more than 10 A. The findings agree with the results obtained with 1H NMR in which the chemical shift and intensity of the methyl groups in the hyperfine shift region of A. ramosus peroxidase were hardly affected by the addition of iodide, unlike the case of horseradish peroxidase. Moreover, 127I NMR and steady-state kinetics showed that the binding of iodide depends on protonation of an amino acid residue with a pKa of about 5.3, which presumably is the distal histidine (His56), 7.8 A away from the iodide ion. The mechanism of electron transfer from the iodide ion to the heme iron is discussed on the basis of these findings.

-	~~{{STRUCTURE_1gza\| PDB=1gza \| SCENE= }}~~	+	Binding of iodide to Arthromyces ramosus peroxidase investigated with X-ray crystallographic analysis, 1H and 127I NMR spectroscopy, and steady-state kinetics.,Fukuyama K, Sato K, Itakura H, Takahashi S, Hosoya T J Biol Chem. 1997 Feb 28;272(9):5752-6. PMID:9038188<ref>PMID:9038188</ref>

-	~~===PEROXIDASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9038188}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1gza]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Eukaryota Eukaryota]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009038188<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Eukaryota]]		[[Category: Eukaryota]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]

OCA: Protected "1gza" [edit=sysop:move=sysop]

OCA — Wed, 21 Nov 2012 15:47:08 GMT

Protected "1gza" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:47, 21 November 2012

OCA at 15:47, 21 November 2012

OCA — Wed, 21 Nov 2012 15:47:06 GMT

←Older revision		Revision as of 15:47, 21 November 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1gza.png\|left\|200px]]		[[Image:1gza.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1gza", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1gza\| PDB=1gza \| SCENE= }}		{{STRUCTURE_1gza\| PDB=1gza \| SCENE= }}

	===PEROXIDASE===		===PEROXIDASE===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9038188}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9038188 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9038188}}		{{ABSTRACT_PUBMED_9038188}}

	==About this Structure==		==About this Structure==
-	~~1GZA~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA].	+	[[1gza]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GZA OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9038188~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009038188</ref><references group="xtra"/>
	[[Category: Eukaryota]]		[[Category: Eukaryota]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
Line 32:		Line 20:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:55:24 2009''