BMRB Entry 17787

Name: Structure of the duplex when (5&#039;S)-8,5&#039;-cyclo-2&#039;-deoxyguanosine is placed opposite dA
Published: 2012-06-25

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PDB ID: 2lfy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17787
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of the duplex when (5'S)-8,5'-cyclo-2'-deoxyguanosine is placed opposite dA

Deposition date:

2011-07-18

Original release date:

2012-06-25

Authors:

Huang, Hai; Das, Rajat; Basu, Ashis; Stone, Michael

Citation:

Citation: Huang, Hai; Das, Rajat; Basu, Ashis; Stone, Michael. "Structures of (5'S)-8,5'-Cyclo-2'-deoxyguanosine Mismatched with dA or dT" Chem. Res. Toxicol. 25, 478-490 (2012).
PubMed: 22309170

Assembly members:

Assembly members:
DNA_(5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3')_, polymer, 12 residues, 2752.830 Da.
DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3')_, polymer, 12 residues, 3031.057 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(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3')_: GTGCGTGTTTGT
DNA_(5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3')_: ACAAACAAGCAC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	164

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D(PTPGPCPTPGPTPTPTP*G)-3')	1
2	DNA (5'-D(PCPAPAPAPCPAPAPGPCPA)-3')	2

Entities:

Entity 1, DNA (5'-D(P*TP*GP*CP*TP*GP*TP*TP*TP*G)-3') 12 residues - 2752.830 Da.

1

DG

DT

DG

DC

DG

DT

DG

DT

2

DG

DT

Entity 2, DNA (5'-D(P*CP*AP*AP*AP*CP*AP*AP*GP*CP*A)-3') 12 residues - 3031.057 Da.

1

DA

DC

DA

DC

DA

DG

DC

2

DA

DC

Samples:

sample_1: DNA (5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3') 1.0 mM; DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3') 1.0 mM; D2O 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

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

NMR spectrometers:

Bruker Avance 800 MHz