BMRB Entry 5739

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PDB ID: 1n1n
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR5739
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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:

Mispairing of the Deoxycytosine with Deoxyadenosine 5' to the 8, 9-Dihydro-8-(N7-guanyl)-9-Hydroxy-Aflatoxin B1 Adduct : Structural study based on NMR

Deposition date:

2003-03-14

Original release date:

2010-07-16

Authors:

Stone, M.; Giri, I.

Citation:

Citation: Giri, I.; Stone, M.. "Wobble dC.dA Pairing 5' to the Cationic Guanine N7 8,9-Dihydro-8-(N7-guanyl)-9-Hydroxyaflatoxin B1 Adduct: Implications for Nontargeted AFB1 Mutagenesis" Biochemistry 42, 7023-7034 (2003).
PubMed: 12795597

Assembly members:

Assembly members:
5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3', polymer, 10 residues, Formula weight is not available
5'-D(*AP*GP*AP*TP*CP*AP*AP*TP*GP*T)-3', polymer, 10 residues, Formula weight is not available
AFN, non-polymer, 330.289 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: .

Entity Sequences (FASTA):

Entity Sequences (FASTA):
5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3': ACATCGATCT
5'-D(*AP*GP*AP*TP*CP*AP*AP*TP*GP*T)-3': AGATCAATGT

Data sets:

assigned_chemical_shifts

Data type	Count
1H chemical shifts	189

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DEOXYRIBONUCLEIC ACID chain A	1
2	DEOXYRIBONUCLEIC ACID chain B	2
3	AFLATOXIN B1	3

Entities:

Entity 1, DEOXYRIBONUCLEIC ACID chain A 10 residues - Formula weight is not available

1

DA

DC

DA

DT

DC

DG

DA

DT

DC

DT

Entity 2, DEOXYRIBONUCLEIC ACID chain B 10 residues - Formula weight is not available

1

DA

DG

DA

DT

DC

DA

DT

DG

DT

Entity 3, AFLATOXIN B1 - C17 H14 O7 - 330.289 Da.

1

AFN

Samples:

sample_1: 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'; 5'-D(*AP*GP*AP*TP*CP*AP*AP*TP*GP*T)-3'; sodium phosphate 0.01 M; NaCl 0.1 M; Na2EDTA 0.05 mM; D2O 99.96%

sample_2: 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'; 5'-D(*AP*GP*AP*TP*CP*AP*AP*TP*GP*T)-3'; sodium phosphate 0.01 M; NaCl 0.1 M; Na2EDTA 0.05 mM; D2O 10%; H2O 90%

sample_cond_1: ionic strength: 0.11 M; pH: 7.2; pressure: 1 atm; temperature: 278 K

sample_cond_2: ionic strength: 0.11 M; pH: 6.7; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	not available	not available	not available
DQF-COSY	not available	not available	not available
P-COSY	not available	not available	not available

Software:

X-PLOR v6.5 - refinement

InsightII v2000 - structure solution

FELIX v97, 2000 - data analysis

MARDIGRAS v5.2, 6.2 - iterative matrix relaxation

AMBER v6.0 - refinement

xwinnmr v3 - collection

NMR spectrometers:

Bruker AVANCE 800 MHz