BMRB Entry 17885

Name: Solution NMR structure of a DNA dodecamer containing the 7-aminomethyl-7-deaza-2'-deoxyguanosine adduct
Published: 2012-08-27

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PDB ID: 2lia
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17885
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution NMR structure of a DNA dodecamer containing the 7-aminomethyl-7-deaza-2'-deoxyguanosine adduct PubMed: 24131376

Deposition date: 2011-08-26 Original release date: 2012-08-27

Authors: Szulik, Marta; Ganguly, Manjori; Wang, Ruo-Wen; Gold, Barry; Stone, Michael

Citation: Szulik, Marta; Voehler, Markus; Ganguly, Manjori; Gold, Barry; Stone, Michael. "Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine." Biochemistry 52, 7659-7668 (2013).

Assembly members:
DNA_dodecamer, polymer, 12 residues, 3005.005 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
DNA_dodecamer: GAGAXCGCTCTC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	73

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(PAPGPAPCPGPCPTPCPTPC)-3')	1

Entities:

Entity 1, DNA (5'-D(P*AP*GP*AP*CP*GP*CP*TP*CP*TP*C)-3') 12 residues - 3005.005 Da.

selfcomplementary

1

DG

DA

DG

DA

2LA

DC

DG

DC

DT

DC

2

DT

DC

Samples:

7amG_sample: DNA dodecamer, [U-2H], 0.25 mM; sodium phosphate 10 mM; sodium chloride 200 mM; sodium azide 0.011 M; sodium EDTA 0.05 mM

7amG_sample_conditions: ionic strength: 0.21 M; pH: 7; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	7amG_sample	isotropic	7amG_sample_conditions
2D 1H-1H COSY	7amG_sample	isotropic	7amG_sample_conditions

Software:

TOPSPIN v2.0.b.6, Bruker Biospin - processing

SPARKY, Goddard - chemical shift assignment

AMBER v10, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

Bruker Avance 800 MHz