BMRB Entry 36641

Name: Structure of guanosine-2&#039;&#039;-fluorinated [d(AACCGGTT)]2
Published: 2025-12-15

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PDB ID: 8y1i
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36641
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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:

Structure of guanosine-2''-fluorinated [d(AACCGGTT)]2

Deposition date:

2024-01-24

Original release date:

2025-12-15

Authors:

Gao, R.; Cao, C.; Tang, G.

Citation:

Citation: Gao, Ruo-Qin; Hu, Xiao-Dong; Zhou, Qiang; Hou, Xian-Feng; Cao, Chunyang; Tang, Gong-Li. "Different DNA Binding and Damage Mode between Anticancer Antibiotics Trioxacarcin A and LL-D49194a1." JACS Au. 4, 3641-3648 (2024).
PubMed: 39328742

Assembly members:

Assembly members:
DNA (5'-D(*(3D1)P*AP*CP*CP*(GF2)P*(GF2)P*TP*T)-3'), polymer, 8 residues, 2382.619 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 2853804 Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*(3D1)P*AP*CP*CP*(GF2)P*(GF2)P*TP*T)-3'): XACCXXTT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	72

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1_1	1
2	entity_1_2	1

Entities:

Entity 1, entity_1_1 8 residues - 2382.619 Da.

1

3D1

DA

DC

GF2

DT

Samples:

sample_1: DNA (5'-D(*(ADE)P*AP*CP*CP*(FGU)P*(FGU)P*TP*T)-3') 2 mM; sodium chloride 20 mM; sodium phosphate 10 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 44.4 mM; pH: 7.2; pressure: 1 atm; temperature: 293 K

Experiments:

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

Software:

NMRFAM-SPARKY, Woonghee Lee,* Marco Tonelli, and John L. Markley* - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - collection

NMRFAM-SPARKY, Woonghee Lee,* Marco Tonelli, and John L. Markley* - peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Agilent Direct Drive 800 MHz