5ktq - Revision history

OCA at 12:42, 6 March 2024

OCA — Wed, 06 Mar 2024 12:42:14 GMT

←Older revision		Revision as of 12:42, 6 March 2024
Line 1:		Line 1:
		+
	==LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP==		==LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP==
-	<StructureSection load='5ktq' size='340' side='right' caption='[[5ktq]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5ktq' size='340' side='right'caption='[[5ktq]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ktq]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_25104 Atcc 25104~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KTQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ktq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KTQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</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]] 2.5Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">TAQ ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&~~id=271 ATCC 25104])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[http~~:~~//en.wikipedia.org/wiki/DNA~~-~~directed_DNA_polymerase DNA~~-~~directed DNA polymerase], with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]~~ </~~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=5ktq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktq OCA], [https://pdbe.org/5ktq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ktq RCSB], [https://www.ebi.ac.uk/pdbsum/5ktq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ktq ProSAT]</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=5ktq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktq OCA], [~~http~~://pdbe.org/5ktq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ktq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ktq PDBsum]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DPO1_THEAQ DPO1_THEAQ]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kt/5ktq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kt/5ktq_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 18:		Line 20:
	</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=5ktq 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=5ktq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structures of the Klenow fragment of the Thermus aquaticus DNA polymerase I (Klentaq1) complexed with four deoxyribonucleoside triphosphates (dNTP) have been determined to 2.5 A resolution. The dNTPs bind adjacent to the O helix of Klentaq1. The triphosphate moieties are at nearly identical positions in all four complexes and are anchored by three positively charged residues, Arg659, Lys663, and Arg587, and by two polar residues, His639 and Gln613. The configuration of the base moieties in the Klentaq1/dNTP complexes demonstrates variability suggesting that dNTP binding is primarily determined by recognition and binding of the phosphate moiety. However, when superimposed on the Taq polymerase/blunt end DNA complex structure (Eom et al., 1996), two of the dNTP/Klentaq1 structures demonstrate appropriate stacking of the nucleotide base with the 3' end of the DNA primer strand, suggesting that at least in these two binary complexes, the observed dNTP conformations are functionally relevant.
-
-	Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates.,Li Y, Kong Y, Korolev S, Waksman G Protein Sci. 1998 May;7(5):1116-23. PMID:9605316<ref>PMID:9605316</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5ktq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[DNA polymerase\|DNA polymerase]]	+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 25104~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~DNA-directed DNA polymerase~~]]	+	[[Category: Thermus aquaticus]]
-	[[Category: Kong, Y]]	+	[[Category: Kong Y]]
-	[[Category: Korolev, S]]	+	[[Category: Korolev S]]
-	[[Category: Li, Y]]	+	[[Category: Li Y]]
-	[[Category: Waksman, G]]	+	[[Category: Waksman G]]
-	~~[[Category: Large fragement of taq dna polymerase i]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:12, 8 February 2016

OCA — Mon, 08 Feb 2016 06:12:28 GMT

←Older revision		Revision as of 06:12, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='5ktq' size='340' side='right' caption='[[5ktq]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5ktq' size='340' side='right' caption='[[5ktq]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ktq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_aquaticus Thermus aquaticus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KTQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ktq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KTQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TAQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ~~Thermus aquaticus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TAQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5ktq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5ktq RCSB], [http://www.ebi.ac.uk/pdbsum/5ktq 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=5ktq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktq OCA], [http://pdbe.org/5ktq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ktq RCSB], [http://www.ebi.ac.uk/pdbsum/5ktq PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=5ktq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 5ktq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 25104]]
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Thermus aquaticus]]
	[[Category: Kong, Y]]		[[Category: Kong, Y]]
	[[Category: Korolev, S]]		[[Category: Korolev, S]]

OCA at 16:46, 10 December 2014

OCA — Wed, 10 Dec 2014 16:46:36 GMT

←Older revision		Revision as of 16:46, 10 December 2014
Line 1:		Line 1:
-	[[~~Image:~~5ktq.~~png~~\|~~left~~\|200px]]	+	==LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP==
		+	<StructureSection load='5ktq' size='340' side='right' caption='[[5ktq]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ktq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KTQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TAQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </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=5ktq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5ktq RCSB], [http://www.ebi.ac.uk/pdbsum/5ktq 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/kt/5ktq_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 crystal structures of the Klenow fragment of the Thermus aquaticus DNA polymerase I (Klentaq1) complexed with four deoxyribonucleoside triphosphates (dNTP) have been determined to 2.5 A resolution. The dNTPs bind adjacent to the O helix of Klentaq1. The triphosphate moieties are at nearly identical positions in all four complexes and are anchored by three positively charged residues, Arg659, Lys663, and Arg587, and by two polar residues, His639 and Gln613. The configuration of the base moieties in the Klentaq1/dNTP complexes demonstrates variability suggesting that dNTP binding is primarily determined by recognition and binding of the phosphate moiety. However, when superimposed on the Taq polymerase/blunt end DNA complex structure (Eom et al., 1996), two of the dNTP/Klentaq1 structures demonstrate appropriate stacking of the nucleotide base with the 3' end of the DNA primer strand, suggesting that at least in these two binary complexes, the observed dNTP conformations are functionally relevant.

-	~~{{STRUCTURE_5ktq\| PDB=5ktq \| SCENE= }}~~	+	Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates.,Li Y, Kong Y, Korolev S, Waksman G Protein Sci. 1998 May;7(5):1116-23. PMID:9605316<ref>PMID:9605316</ref>

-	~~===LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9605316}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[5ktq]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_aquaticus Thermus aquaticus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA].~~	+

	==See Also==		==See Also==
	*[[DNA polymerase\|DNA polymerase]]		*[[DNA polymerase\|DNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009605316<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
-	[[Category: Kong, Y.]]	+	[[Category: Kong, Y]]
-	[[Category: Korolev, S.]]	+	[[Category: Korolev, S]]
-	[[Category: Li, Y.]]	+	[[Category: Li, Y]]
-	[[Category: Waksman, G.]]	+	[[Category: Waksman, G]]
	[[Category: Large fragement of taq dna polymerase i]]		[[Category: Large fragement of taq dna polymerase i]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:12, 20 October 2012

OCA — Sat, 20 Oct 2012 09:12:14 GMT

←Older revision		Revision as of 09:12, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[5ktq]] is a 1 chain structure ~~of [[DNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA].	+	[[5ktq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA].

	==See Also==		==See Also==

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

OCA — Wed, 25 Jul 2012 22:05:30 GMT

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

←Older revision

Revision as of 22:05, 25 July 2012

OCA at 22:05, 25 July 2012

OCA — Wed, 25 Jul 2012 22:05:29 GMT

←Older revision		Revision as of 22:05, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:5ktq.png\|left\|200px]]		[[Image:5ktq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_5ktq", 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_5ktq\| PDB=5ktq \| SCENE= }}		{{STRUCTURE_5ktq\| PDB=5ktq \| SCENE= }}

	===LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP===		===LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9605316}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9605316 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9605316}}		{{ABSTRACT_PUBMED_9605316}}

	==About this Structure==		==About this Structure==
-	~~5KTQ~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA].	+	[[5ktq]] is a 1 chain structure of [[DNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA].
		+
		+	==See Also==
		+	*[[DNA polymerase\|DNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9605316~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009605316</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
Line 31:		Line 22:
	[[Category: Waksman, G.]]		[[Category: Waksman, G.]]
	[[Category: Large fragement of taq dna polymerase i]]		[[Category: Large fragement of taq dna polymerase i]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 19:42:46 2009''~~	+

OCA at 17:42, 16 February 2009

OCA — Mon, 16 Feb 2009 17:42:47 GMT

←Older revision		Revision as of 17:42, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	5KTQ is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA].	+	5KTQ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KTQ OCA].

	==Reference==		==Reference==
-	Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates., Li Y, Kong Y, Korolev S, Waksman G, Protein Sci. 1998 May;7(5):1116-23. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9605316 9605316]~~	+	<ref group="xtra">PMID:9605316</ref><references group="xtra"/>
	[[Category: DNA-directed DNA polymerase]]		[[Category: DNA-directed DNA polymerase]]
-	[[Category: Single protein]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
	[[Category: Kong, Y.]]		[[Category: Kong, Y.]]
Line 33:		Line 32:
	[[Category: Large fragement of taq dna polymerase i]]		[[Category: Large fragement of taq dna polymerase i]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 14~~:05:~~13 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:42:46 2009''

OCA at 11:05, 3 July 2008

OCA — Thu, 03 Jul 2008 11:05:13 GMT

←Older revision		Revision as of 11:05, 3 July 2008
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-	[[Image:5ktq.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:5ktq.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_5ktq\| PDB=5ktq \| SCENE= }}		{{STRUCTURE_5ktq\| PDB=5ktq \| SCENE= }}

-	~~'''~~LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP~~'''~~	+	===LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP===


-	~~==Overview==~~	+	<!--
-	The crystal structures of the Klenow fragment of the Thermus aquaticus DNA polymerase I (Klentaq1) complexed with four deoxyribonucleoside triphosphates (dNTP) have been determined to 2.5 A resolution. The dNTPs bind adjacent to the O helix of Klentaq1. The triphosphate moieties are at nearly identical positions in all four complexes and are anchored by three positively charged residues, ~~Arg659~~, ~~Lys663, and Arg587, and by two polar residues, His639 and Gln613. The configuration of~~ the ~~base moieties in~~ the ~~Klentaq1/dNTP complexes demonstrates variability suggesting that dNTP binding is primarily determined by recognition and binding of the phosphate moiety. However, when superimposed~~ on ~~the Taq polymerase~~/~~blunt end DNA complex structure (Eom et al~~.~~, 1996~~), ~~two of the dNTP/Klentaq1 structures demonstrate appropriate stacking of the nucleotide base with the 3' end of the DNA primer strand, suggesting that at least in these two binary complexes,~~ the ~~observed dNTP conformations are functionally relevant~~.	+	The line below this paragraph, {{ABSTRACT_PUBMED_9605316}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9605316 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9605316}}

	==About this Structure==		==About this Structure==
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	[[Category: Waksman, G.]]		[[Category: Waksman, G.]]
	[[Category: Large fragement of taq dna polymerase i]]		[[Category: Large fragement of taq dna polymerase i]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:35:34 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 14:05:13 2008''

OCA at 19:35, 4 May 2008

OCA — Sun, 04 May 2008 19:35:35 GMT

←Older revision		Revision as of 19:35, 4 May 2008
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	[[Image:5ktq.gif\|left\|200px]]		[[Image:5ktq.gif\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 5ktq \|SIZE=350\|CAPTION=~~ <~~scene name='initialview01'>5ktq</scene>, resolution 2.50Å~~	+	The line below this paragraph, containing "STRUCTURE_5ktq", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=DCP:2'~~-~~DEOXYCYTIDINE~~-~~5'-TRIPHOSPHATE'>DCP</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase]~~, ~~with EC number [http://www~~.~~brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span>~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE= TAQ~~ (~~[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus]~~)	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_5ktq\| PDB=5ktq \| SCENE= }}
-	~~\|RELATEDENTRY=~~	+
-	~~\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca~~-~~docs/fgij/fg.htm?mol=5ktq FirstGlance], [http://oca.weizmann.ac.il/oca~~-~~bin/ocaids?id~~=5ktq ~~OCA], [http://www.ebi.ac.uk/pdbsum/5ktq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId~~=~~5ktq RCSB]</span>~~	+
-	}}	+

	'''LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP'''		'''LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP'''
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	[[Category: Li, Y.]]		[[Category: Li, Y.]]
	[[Category: Waksman, G.]]		[[Category: Waksman, G.]]
-	[[Category: ~~large~~ fragement of taq dna polymerase i]]	+	[[Category: Large fragement of taq dna polymerase i]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:35:34 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:41:42 2008''	+

OCA at 02:41, 31 March 2008

OCA — Mon, 31 Mar 2008 02:41:42 GMT

←Older revision		Revision as of 02:41, 31 March 2008
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	\|SITE=		\|SITE=
	\|LIGAND= <scene name='pdbligand=DCP:2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE'>DCP</scene>		\|LIGAND= <scene name='pdbligand=DCP:2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE'>DCP</scene>
-	\|ACTIVITY= [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7]	+	\|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span>
	\|GENE= TAQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])		\|GENE= TAQ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ktq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ktq OCA], [http://www.ebi.ac.uk/pdbsum/5ktq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=5ktq RCSB]</span>
	}}		}}

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	[[Category: Li, Y.]]		[[Category: Li, Y.]]
	[[Category: Waksman, G.]]		[[Category: Waksman, G.]]
-	[[Category: DCP]]
	[[Category: large fragement of taq dna polymerase i]]		[[Category: large fragement of taq dna polymerase i]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun~~ Mar ~~23 16:~~05:30 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:41:42 2008''