4hqi - Revision history

OCA at 11:43, 1 March 2024

2024-03-01T11:43:06Z

←Older revision		Revision as of 11:43, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4hqi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HQI FirstGlance]. <br>		<table><tr><td colspan='2'>[[4hqi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HQI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BZG:6-(BENZYLOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>BZG</scene>, <scene name='pdbligand=D3N:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-1H-PERIMIDIN-2(3H)-ONE'>D3N</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BZG:6-(BENZYLOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>BZG</scene>, <scene name='pdbligand=D3N:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-1H-PERIMIDIN-2(3H)-ONE'>D3N</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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=4hqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqi OCA], [https://pdbe.org/4hqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hqi RCSB], [https://www.ebi.ac.uk/pdbsum/4hqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqi 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=4hqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqi OCA], [https://pdbe.org/4hqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hqi RCSB], [https://www.ebi.ac.uk/pdbsum/4hqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqi ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The 2'-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H )-one] (dPer) recognizes in DNA the O6-benzyl-2'-deoxyguanosine nucleoside (O6-Bn-dG), formed by exposure to N-benzylmethylnitrosamine. Herein, we show how dPer distinguishes between O6-Bn-dG and dG in DNA. The structure of the modified Dickerson-Drew dodecamer (DDD) in which guanine at position G4 has been replaced by O6-Bn-dG and cytosine C9 has been replaced with dPer to form the modified O6-Bn-dG:dPer (DDD-XY) duplex [5'-d(C1G2C3X4A5A6T7T8Y9G10C11G12)-3']2 (X = O6-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond. This provides a binding pocket that allows the benzyl group of O6-Bn-dG to intercalate between Per and thymine of the 3'-neighbor A:T base pair. Nuclear magnetic resonance data suggest that a similar intercalative recognition mechanism applies in this sequence in solution. However, in solution, the benzyl ring of O6-Bn-dG undergoes rotation on the nuclear magnetic resonance time scale. In contrast, the structure of the modified DDD in which cytosine at position C9 is replaced with dPer to form the dG:dPer (DDD-GY) [5'-d(C1G2C3G4A5A6T7T8Y9G10C11G12)-3']2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.
-
-	Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.,Kowal EA, Lad RR, Pallan PS, Dhummakupt E, Wawrzak Z, Egli M, Sturla SJ, Stone MP Nucleic Acids Res. 2013 Jun 8. PMID:23748954<ref>PMID:23748954</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4hqi" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:04, 9 November 2022

2022-11-09T08:04:51Z

←Older revision		Revision as of 08:04, 9 November 2022
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	<StructureSection load='4hqi' size='340' side='right'caption='[[4hqi]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='4hqi' size='340' side='right'caption='[[4hqi]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4hqi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4HQI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4hqi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HQI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BZG:6-(BENZYLOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>BZG</scene>, <scene name='pdbligand=D3N:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-1H-PERIMIDIN-2(3H)-ONE'>D3N</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
-	~~<tr~~ id~~='NonStdRes'><td class~~="~~sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat~~"><scene name='pdbligand=BZG:6-(BENZYLOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>BZG</scene>, <scene name='pdbligand=D3N:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-1H-PERIMIDIN-2(3H)-ONE'>D3N</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=4hqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqi OCA], [https://pdbe.org/4hqi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hqi RCSB], [https://www.ebi.ac.uk/pdbsum/4hqi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqi 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=4hqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqi OCA], [~~http~~://pdbe.org/4hqi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4hqi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4hqi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqi ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Egli, M]]	+	[[Category: Synthetic construct]]
-	[[Category: Kowal~~, E A~~]]	+	[[Category: Egli M]]
-	[[Category: Lad, R]]	+	[[Category: Kowal EA]]
-	[[Category: Muffly, E]]	+	[[Category: Lad R]]
-	[[Category: Pallan~~, P S~~]]	+	[[Category: Muffly E]]
-	[[Category: Stone~~, M P~~]]	+	[[Category: Pallan PS]]
-	[[Category: Sturla~~, S J~~]]	+	[[Category: Stone MP]]
-	[[Category: Wawrzak, Z]]	+	[[Category: Sturla SJ]]
-	~~[[Category: B-form dna]]~~	+	[[Category: Wawrzak Z]]
-	~~[[Category: Dickerson-drew dodecamer]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dper]]~~	+
-	~~[[Category: O6-benzyl-2'-deoxyguanosine]]~~	+
-	~~[[Category: Perimidinone-derived nucleoside~~]]	+

OCA at 07:19, 27 March 2019

2019-03-27T07:19:13Z

←Older revision		Revision as of 07:19, 27 March 2019
Line 1:		Line 1:

	==Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex==		==Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex==
-	<StructureSection load='4hqi' size='340' side='right' caption='[[4hqi]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='4hqi' size='340' side='right'caption='[[4hqi]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4hqi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HQI FirstGlance]. <br>		<table><tr><td colspan='2'>[[4hqi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HQI FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Egli, M]]		[[Category: Egli, M]]
	[[Category: Kowal, E A]]		[[Category: Kowal, E A]]

OCA at 07:54, 5 August 2016

2016-08-05T07:54:57Z

←Older revision		Revision as of 07:54, 5 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_4hqi\| PDB=4hqi \| SCENE= }}
-	===Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex===
-	{{ABSTRACT_PUBMED_23748954}}

-	==~~About this~~ Structure==	+	==Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex==
-	[[4hqi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQI OCA].	+	<StructureSection load='4hqi' size='340' side='right' caption='[[4hqi]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4hqi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HQI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BZG:6-(BENZYLOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>BZG</scene>, <scene name='pdbligand=D3N:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-1H-PERIMIDIN-2(3H)-ONE'>D3N</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=4hqi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hqi OCA], [http://pdbe.org/4hqi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4hqi RCSB], [http://www.ebi.ac.uk/pdbsum/4hqi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4hqi ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The 2'-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H )-one] (dPer) recognizes in DNA the O6-benzyl-2'-deoxyguanosine nucleoside (O6-Bn-dG), formed by exposure to N-benzylmethylnitrosamine. Herein, we show how dPer distinguishes between O6-Bn-dG and dG in DNA. The structure of the modified Dickerson-Drew dodecamer (DDD) in which guanine at position G4 has been replaced by O6-Bn-dG and cytosine C9 has been replaced with dPer to form the modified O6-Bn-dG:dPer (DDD-XY) duplex [5'-d(C1G2C3X4A5A6T7T8Y9G10C11G12)-3']2 (X = O6-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond. This provides a binding pocket that allows the benzyl group of O6-Bn-dG to intercalate between Per and thymine of the 3'-neighbor A:T base pair. Nuclear magnetic resonance data suggest that a similar intercalative recognition mechanism applies in this sequence in solution. However, in solution, the benzyl ring of O6-Bn-dG undergoes rotation on the nuclear magnetic resonance time scale. In contrast, the structure of the modified DDD in which cytosine at position C9 is replaced with dPer to form the dG:dPer (DDD-GY) [5'-d(C1G2C3G4A5A6T7T8Y9G10C11G12)-3']2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.

-	~~==Reference==~~	+	Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.,Kowal EA, Lad RR, Pallan PS, Dhummakupt E, Wawrzak Z, Egli M, Sturla SJ, Stone MP Nucleic Acids Res. 2013 Jun 8. PMID:23748954<ref>PMID:23748954</ref>
-	<ref ~~group="xtra"~~>PMID:~~023748954~~</ref><~~references group~~="~~xtra~~"/><references/>	+
-	[[Category: Egli, M.]]	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: Kowal, E A.]]	+	</div>
-	[[Category: Lad, R.]]	+	<div class="pdbe-citations 4hqi" style="background-color:#fffaf0;"></div>
-	[[Category: Muffly, E.]]	+	== References ==
-	[[Category: Pallan, P S.]]	+	<references/>
-	[[Category: Stone, M P.]]	+	__TOC__
-	[[Category: Sturla, S J.]]	+	</StructureSection>
-	[[Category: Wawrzak, Z.]]	+	[[Category: Egli, M]]
		+	[[Category: Kowal, E A]]
		+	[[Category: Lad, R]]
		+	[[Category: Muffly, E]]
		+	[[Category: Pallan, P S]]
		+	[[Category: Stone, M P]]
		+	[[Category: Sturla, S J]]
		+	[[Category: Wawrzak, Z]]
	[[Category: B-form dna]]		[[Category: B-form dna]]
	[[Category: Dickerson-drew dodecamer]]		[[Category: Dickerson-drew dodecamer]]

OCA at 15:36, 10 July 2013

2013-07-10T15:36:49Z

←Older revision		Revision as of 15:36, 10 July 2013
Line 1:		Line 1:
-	'~~''Unreleased structure'''~~	+	{{STRUCTURE_4hqi\| PDB=4hqi \| SCENE= }}
		+	===Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex===
		+	{{ABSTRACT_PUBMED_23748954}}

-	~~The entry~~ 4hqi is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4hqi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HQI OCA].

-	~~Authors~~: Kowal, E.A., Lad, R., Pallan, P.S.~~, Muffly, E., Wawrzak, Z., Egli~~, M., Sturla, S.J., ~~Stone, M.P~~.	+	==Reference==
-		+	<ref group="xtra">PMID:023748954</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Structure of~~ O6-~~Benzyl~~-2'-deoxyguanosine ~~opposite perimidinone~~-derived ~~synthetic~~ nucleoside ~~in DNA duplex~~	+	[[Category: Egli, M.]]
		+	[[Category: Kowal, E A.]]
		+	[[Category: Lad, R.]]
		+	[[Category: Muffly, E.]]
		+	[[Category: Pallan, P S.]]
		+	[[Category: Stone, M P.]]
		+	[[Category: Sturla, S J.]]
		+	[[Category: Wawrzak, Z.]]
		+	[[Category: B-form dna]]
		+	[[Category: Dickerson-drew dodecamer]]
		+	[[Category: Dna]]
		+	[[Category: Dper]]
		+	[[Category: O6-benzyl-2'-deoxyguanosine]]
		+	[[Category: Perimidinone-derived nucleoside]]

OCA at 09:06, 21 November 2012

2012-11-21T09:06:02Z

←Older revision		Revision as of 09:06, 21 November 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4hqi is ON HOLD	+	The entry 4hqi is ON HOLD until Paper Publication

	Authors: Kowal, E.A., Lad, R., Pallan, P.S., Muffly, E., Wawrzak, Z., Egli, M., Sturla, S.J., Stone, M.P.		Authors: Kowal, E.A., Lad, R., Pallan, P.S., Muffly, E., Wawrzak, Z., Egli, M., Sturla, S.J., Stone, M.P.

	Description: Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex		Description: Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex

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

2012-10-31T08:44:34Z

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

←Older revision

Revision as of 08:44, 31 October 2012

OCA: New page: '''Unreleased structure''' The entry 4hqi is ON HOLD Authors: Kowal, E.A., Lad, R., Pallan, P.S., Muffly, E., Wawrzak, Z., Egli, M., Sturla, S.J., Stone, M.P. Description: Structure of...

2012-10-31T08:44:33Z

New page: '''Unreleased structure''' The entry 4hqi is ON HOLD Authors: Kowal, E.A., Lad, R., Pallan, P.S., Muffly, E., Wawrzak, Z., Egli, M., Sturla, S.J., Stone, M.P. Description: Structure of...

New page

'''Unreleased structure'''

The entry 4hqi is ON HOLD

Authors: Kowal, E.A., Lad, R., Pallan, P.S., Muffly, E., Wawrzak, Z., Egli, M., Sturla, S.J., Stone, M.P.

Description: Structure of O6-Benzyl-2'-deoxyguanosine opposite perimidinone-derived synthetic nucleoside in DNA duplex