BMRB Entry 34805

Name: Solution structure of the 8-17 DNAzyme in presence of Zn2+
Published: 2023-04-19

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PDB ID: 8or8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34805
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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:

Solution structure of the 8-17 DNAzyme in presence of Zn2+

Deposition date:

2023-04-13

Original release date:

2023-04-19

Authors:

Andralojc, W.; Gdaniec, Z.

Citation:

Citation: Wieruszewska, Julia; Pawlowicz, Aleksandra; Polomska, Ewa; Pasternak, Karol; Gdaniec, Zofia; Andralojc, Witold. "The 8-17 DNAzyme can operate in a single active structure regardless of metal ion cofactor" Nat. Commun. 15, 4218-4218 (2024).
PubMed: 38760331

Assembly members:

Assembly members:
entity_1, polymer, 35 residues, 10841.923 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: CGCCGGGGTCGAAGACTGCC AGCGGCTCGACGGCG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
1H chemical shifts	302
31P chemical shifts	32

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 35 residues - 10841.923 Da.

1

DC

DG

DC

DG

DT

DC

2

DG

DA

DG

DA

DC

DT

DG

DC

3

DA

DG

DC

DG

DC

DT

DC

DG

DA

4

DC

DG

DC

DG

Samples:

sample_1: 8-17 DNAzyme 2.2 mM; cacodylate 10 mM; zinc chloride 4 mM; sodium chloride 200 mM

sample_2: 8-17 DNAzyme 2.2 mM; cacodylate 10 mM; zinc chloride 4 mM; sodium chloride 200 mM

sample_conditions_1: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 200 mM; pH: 6.0; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-31P COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2

Software:

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

NMRFAM-SPARKY, NMRFAM - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 700 MHz