BMRB Entry 25531

Name: N2-dG-IQ modified DNA at the G1 position of the NarI recognition sequence
Published: 2016-03-29

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PDB ID: 2n0q
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25531
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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:

N2-dG-IQ modified DNA at the G1 position of the NarI recognition sequence

Deposition date:

2015-03-11

Original release date:

2016-03-29

Authors:

Stavros, Kallie; Hawkins, Edward; Rizzo, Carmelo; Stone, Michael

Citation:

Citation: Stavros, Kallie; Hawkins, Edward; Rizzo, Carmelo; Stone, Michael. "Base-Displaced Intercalated Conformation of the 2-Amino-3-methylimidazo[4,5-f]quinoline N(2)-dG DNA Adduct Positioned at the Nonreiterated G(1) in the NarI Restriction Site" Chem. Res. Toxicol. 28, 1455-1468 (2015).
PubMed: 26083477

Assembly members:

Assembly members:
DNA_(5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3'), polymer, 12 residues, 3251.149 Da.
DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'), polymer, 12 residues, 3728.459 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*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3'): CTCXGCGCCATC
DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'): GATGGCGCCGAG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	156

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(CPTPCP(IQG)PGPCPGPCPCPAPTPC)-3')	1
2	DNA (5'-D(GPAPTPGPGPCPGPCPCPGPAPG)-3')	2

Entities:

Entity 1, DNA (5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3') 12 residues - 3251.149 Da.

1

DC

DT

DC

IQG

DG

DC

DG

DC

DA

2

DT

DC

Entity 2, DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') 12 residues - 3728.459 Da.

1

DG

DA

DT

DG

DC

DG

DC

DG

2

DA

DG

Samples:

sample_1: DNA (5'-D(*CP*TP*CP*(IQG)P*GP*CP*GP*CP*CP*AP*TP*C)-3') 430 mM; DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') 430 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 288 K

Experiments:

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

Software:

TOPSPIN, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, data analysis

MARDIGRAS, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - chemical shift calculation

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

NMR spectrometers:

Bruker Avance 900 MHz