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2qeg

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B-DNA with 7-deaza-dG modification

Structural highlights

2qeg is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.6Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Site-specific insertion of 5-(3-aminopropyl)-2'-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7)T (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19)T (20)C (21) Z (22)C (23)G (24))-3' (named DDD (Z10)) and 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7) X (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19) X (20)C (21) Z (22)C (23)G (24))-3' (named DDD (2+Z10)) (X = Z3dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD (2+Z10) duplex reveals that the tethered cations at base pairs A (5).X (20) and X (8).A (17) extend within the major groove in the 3'-direction, toward conserved Mg (2+) binding sites located adjacent to N+2 base pairs C (3).Z (22) and Z (10).C (15). Bridging waters located between the tethered amines and either Z (10) or Z (22) O (6) stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD (2+Z10) duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z (10) O (6) and Z (22) O (6). The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C.G base pair, facilitating interstrand cross-linking.

A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards.,Wang F, Li F, Ganguly M, Marky LA, Gold B, Egli M, Stone MP Biochemistry. 2008 Jul 8;47(27):7147-57. Epub 2008 Jun 13. PMID:18549246^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang F, Li F, Ganguly M, Marky LA, Gold B, Egli M, Stone MP. A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards. Biochemistry. 2008 Jul 8;47(27):7147-57. Epub 2008 Jun 13. PMID:18549246 doi:http://dx.doi.org/10.1021/bi800375m

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2qeg"

@@ Line 1: / Line 1: @@
 ==B-DNA with 7-deaza-dG modification==
-<StructureSection load='2qeg' size='340' side='right' caption='[[2qeg]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='2qeg' size='340' side='right'caption='[[2qeg]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qeg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QEG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qeg]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QEG FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=7GU:7-DEAZA-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>7GU</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]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2qef|2qef]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7GU:7-DEAZA-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>7GU</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=2qeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qeg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qeg RCSB], [http://www.ebi.ac.uk/pdbsum/2qeg PDBsum]</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=2qeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qeg OCA], [https://pdbe.org/2qeg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qeg RCSB], [https://www.ebi.ac.uk/pdbsum/2qeg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qeg ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 15: / Line 16: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2qeg" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Egli, M]]
+[[Category: Large Structures]]
-[[Category: Ganguly, M]]
+[[Category: Egli M]]
-[[Category: Gold, B]]
+[[Category: Ganguly M]]
-[[Category: Li, F]]
+[[Category: Gold B]]
-[[Category: Marky, L A]]
+[[Category: Li F]]
-[[Category: Stone, M P]]
+[[Category: Marky LA]]
-[[Category: Wang, F]]
+[[Category: Stone MP]]
-[[Category: 7-deaza-dg]]
+[[Category: Wang F]]
-[[Category: B-dna]]
-[[Category: Dna]]

2qeg

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Current revision

B-DNA with 7-deaza-dG modification

Structural highlights

Publication Abstract from PubMed

References

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