BMRB Entry 19375

Name: NMR Structure of N2-IQ-dG at the G3 position in the NarI recognition sequence
Published: 2014-05-12

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PDB ID: 2mav
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19375
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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 Structure of N2-IQ-dG at the G3 position in the NarI recognition sequence

Deposition date:

2013-07-19

Original release date:

2014-05-12

Authors:

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

Citation:

Citation: Stavros, Kallie; Hawkins, Edward; Rizzo, Carmelo; Stone, Michael. "Base-displaced intercalation of the 2-amino-3-methylimidazo[4,5-f]quinolone N2-dG adduct in the NarI DNA recognition sequence" Nucleic Acids Res. 42, 3450-3463 (2014).
PubMed: 24366876

Assembly members:

Assembly members:
DNA_(5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3'), polymer, 12 residues, 3777.5 Da.
DNA_(5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'), polymer, 12 residues, 3711.459 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*GP*GP*CP*GP*CP*CP*AP*TP*C)-3'): CTCGGCXCCATC
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
homonucl_NOEs
- homonuclear_NOE_list_1

Data type	Count
1H chemical shifts	213
homonuclear NOE values	334

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(CPTPCPGPGPCPGPCPCPAPTPC)-3')	1
2	DNA (5'-D(GPAPTPGPGPCPGPCPCPGPAPG)-3')	2

Entities:

Entity 1, DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3') 12 residues - 3777.5 Da.

Oligo was synthesized as described in J. Stover, C. Rizzo [Chem. Res. Toxicol., 2007, 20, 1972-1979]

1

DC

DT

DC

DG

DC

IQG

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 - 3711.459 Da.

Oligo was obtained from Midland Certified Reagent Co. and purified by RP-HPLC.

1

DG

DA

DT

DG

DC

DG

DC

DG

2

DA

DG

Samples:

sample_1: DNA (5'-D(*CP*TP*CP*GP*GP*CP*IQGP*CP*CP*AP*TP*C)-3') 560 nM; DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3') 560 nM

sample_2: DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3') 560 mM; DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*CP*AP*TP*C)-3') 560 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 v3.2, Bruker Biospin - collection, processing

SPARKY v3.115, Goddard - chemical shift assignment, data analysis, peak picking

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure solution

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

MARDIGRAS, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - data analysis

NMR spectrometers:

Bruker DRX 800 MHz