BMRB Entry 18199

Name: Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA. Structure of a Thymine bulge.
Published: 2012-05-08

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PDB ID: 2lo5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR18199
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA. Structure of a Thymine bulge.

Deposition date:

2012-01-23

Original release date:

2012-05-08

Authors:

Morrow, Janet; Fountain, Matthew; del Mundo, Imee Marie; Siter, Kevin

Citation:

Citation: Del Mundo, Imee Marie A; Siters, Kevin; Fountain, Matthew; Morrow, Janet. "Structural Basis for Bifunctional Zinc(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA." Inorg. Chem. 51, 5444-5457 (2012).
PubMed: 22507054

Assembly members:

Assembly members:
DNA_1, polymer, 12 residues, 3664.409 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_1: GGCCGCAGTGCC

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	55

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA_1	1

Entities:

Entity 1, DNA_1 12 residues - 3664.409 Da.

1

DG

DC

DG

DC

DA

DG

DT

DG

2

DC

Samples:

sample_1: DNA_1 1.8 mM; D2O 100%; NaCl 0.1 M; HEPES 0.02 M

sample_2: DNA_1 1.8 mM; H2O 90%; D2O 10%; NaCl 0.1 M; HEPES 0.02 M

sample_conditions_1: ionic strength: 0.1 M; pD: 7.9; pressure: 1 atm; temperature: 273 K

sample_conditions_2: ionic strength: 0.1 M; pD: 7.9; pressure: 1 atm; temperature: 288 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2

Software:

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - geometry optimization

SPARKY v3.14, Goddard - chemical shift assignment, data analysis

NMR spectrometers:

Varian INOVA 500 MHz