BMRB Entry 6009

Name: NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+
Published: 2010-07-16

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PDB ID: 1rde
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR6009
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+ PubMed: 15214802

Deposition date: 2003-11-18 Original release date: 2010-07-16

Authors: Mao, X.; Marky, L.; Gmeiner, W.

Citation: Mao, X.; Marky, L.; Gmeiner, W.. "NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+" J. Biomol. Struct. Dyn. 22, 25-33 (2004).

Assembly members:
thrombin binding 15mer DNA aptamer, polymer, 15 residues, 4600 Da.
SR, non-polymer, 87.620 Da.

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
thrombin binding 15mer DNA aptamer: GGTTGGTGTGGTTGG

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1

Data type	Count
31P chemical shifts	14

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Thrombin-binding DNA aptamer	1
2	Strontium (II) ion	2

Entities:

Entity 1, Thrombin-binding DNA aptamer 15 residues - 4600 Da.

1

DG

DT

DG

DT

DG

DT

DG

2

DG

DT

DG

Entity 2, Strontium (II) ion - Sr - 87.620 Da.

1

SR

Samples:

sample_1: thrombin binding 15mer DNA aptamer 1 mM; SRONTIUM (II) ION1 – 1.3 mM; D2O 100%

sample_2: thrombin binding 15mer DNA aptamer 1 mM; SRONTIUM (II) ION1 – 1.3 mM; H2O 90%; D2O 10%

sample_cond_1: ionic strength: 3 mM; pH: 4.7; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	not available	not available	sample_cond_1
2D TOCSY	not available	not available	sample_cond_1
E-COSY	not available	not available	sample_cond_1
P31-H1 COSY	not available	not available	sample_cond_1
ROESY	not available	not available	sample_cond_1

Software:

CNS - refinement

NMR spectrometers:

Bruker AVANCE 600 MHz