BMRB Entry 18762

Name: NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing
Published: 2012-11-20

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PDB ID: 2lzk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18762
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing

Deposition date:

2012-10-04

Original release date:

2012-11-20

Authors:

Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin; Cai, Yuqin; Rodriguez, Fabian; Sayer, Jane; Jerina, Donald; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas

Citation:

Citation: Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin; Cai, Yuqin; Rodriguez, Fabian; Sayer, Jane; Jerina, Donald; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas. "Nuclear Magnetic Resonance Solution Structure of an N(2)-Guanine DNA Adduct Derived from the Potent Tumorigen Dibenzo[a,l]pyrene: Intercalation from the Minor Groove with Ruptured Watson-Crick Base Pairing." Biochemistry 51, 9751-9762 (2012).
PubMed: 23121427

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*CP*GP*AP*TP*GP*G)-3')_, polymer, 11 residues, 3454.286 Da.
1,3-DIAMINOBENZYL PHENYLALANINE, non-polymer, 122.168 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*CP*GP*AP*TP*GP*G)-3')_: GGTAGCGATGG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	154

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(GPGPTPAPGPCPGPAPTPGP*G)-3')	2
3	1,3-DIAMINOBENZYL PHENYLALANINE	3

Entities:

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

C14 ATOM OF DB[a,l]P LINKED TO N2 ATOM OF DG6

1

DC

DA

DT

DC

DG

DC

DT

DA

DC

2

DC

Entity 2, DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3') 11 residues - 3454.286 Da.

1

DG

DT

DA

DG

DC

DG

DA

DT

DG

2

DG

Entity 3, 1,3-DIAMINOBENZYL PHENYLALANINE - C7 H10 N2 - 122.168 Da.

1

DBP

Samples:

sample_1: DNA duplex 1.5 mM; sodium phosphate 10 mM; sodium chloride 100 mM; DSS 25 nM; D2O 100%

sample_2: DNA duplex 1.5 mM; sodium phosphate 10 mM; sodium chloride 100 mM; DSS 25 nM; 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

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis

NMR spectrometers:

Bruker Avance 500 MHz