BMRB Entry 19695

Name: NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations
Published: 2014-03-31

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PDB ID: 2miv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19695
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR studies of N2-guanine adducts derived from the tumorigen dibenzo[a,l]pyrene in DNA: Impact of adduct stereochemistry, size, and local DNA structure on solution conformations

Deposition date:

2013-12-20

Original release date:

2014-03-31

Authors:

Rodriguez, Fabian; Liu, Zhi; Lin, Chin; Ding, Shuang; Cai, Yuqin; Kolbanovskiy, Alexander; Kolbanovskiy, Marina; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas

Citation:

Citation: Rodriguez, Fabian; Liu, Zhi; Lin, Chin; Ding, Shuang; Cai, Yuqin; Kolbanovskiy, Alexander; Kolbanovskiy, Marina; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas. "Nuclear Magnetic Resonance Studies of an N(2)-Guanine Adduct Derived from the Tumorigen Dibenzo[a,l]pyrene in DNA: Impact of Adduct Stereochemistry, Size, and Local DNA Sequence on Solution Conformations" Biochemistry 53, 1827-1841 (2014).
PubMed: 24617538

Assembly members:

Assembly members:
DNA_(5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3'), polymer, 11 residues, 3254.165 Da.
DNA_(5'-D(*GP*GP*TP*AP*GP*GP*AP*TP*GP*G)-3'), polymer, 10 residues, 3165.103 Da.
(11R,12R,13R)-11,12,13,14-tetrahydronaphtho[1,2,3,4-pqr]tetraphene-11,12,13-triol, non-polymer, 354.398 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_(5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3'): CCATCGCTACC
DNA_(5'-D(*GP*GP*TP*AP*GP*GP*AP*TP*GP*G)-3'): GGTAGGATGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	151

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(CPCPAPTPCPGPCPTPAPCP*C)-3')	1
2	DNA (5'-D(GPGPTPAPGPGPAPTPGPG)-3')	2
3	(11R,12R,13R)-11,12,13,14-tetrahydronaphtho[1,2,3,4-pqr]tetraphene-11,12,13-triol	3

Entities:

Entity 1, DNA (5'-D(*CP*CP*AP*TP*CP*GP*CP*TP*AP*CP*C)-3') 11 residues - 3254.165 Da.

1

DC

DA

DT

DC

DG

DC

DT

DA

DC

2

DC

Entity 2, DNA (5'-D(*GP*GP*TP*AP*GP*GP*AP*TP*GP*G)-3') 10 residues - 3165.103 Da.

1

DG

DT

DA

DG

DA

DT

DG

Entity 3, (11R,12R,13R)-11,12,13,14-tetrahydronaphtho[1,2,3,4-pqr]tetraphene-11,12,13-triol - C24 H18 O3 - 354.398 Da.

1

2QL

Samples:

sample_1: DB[a,l]P covalently bound to 11mer DNA duplex 1.5 mM; NaCl 100 mM; Na2HPO4 10 mM; DSS 25 mM; D2O 100%

sample_2: DB[a,l]P covalently bound to 11mer DNA duplex 1.5 mM; NaCl 100 mM; Na2HPO4 10 mM; DSS 25 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.8

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment, data analysis

TOPSPIN, Bruker Biospin - collection

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

Bruker Avance 500 MHz