BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17422

Title: Solution Structure of a DNA Duplex Containing the Potent Anti-Poxvirus Agent Cidofovir   PubMed: 21280608

Authors: Julien, Olivier; Beadle, James; Magee, Wendy; Chatterjee, Subhrangsu; Hostetler, Karl; Evans, David; Sykes, Brian

Citation: Julien, Olivier; Beadle, James; Magee, Wendy; Chatterjee, Subhrangsu; Hostetler, Karl; Evans, David; Sykes, Brian. "Solution structure of a DNA duplex containing the potent anti-poxvirus agent cidofovir."  J. Am. Chem. Soc. 133, 2264-2274 (2011).

Assembly members:
Cidofovir_DNA_duplex_chain_A, polymer, 12 residues, Formula weight is not available
Cidofovir_DNA_duplex_chain_B, polymer, 12 residues, Formula weight is not available

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):
Cidofovir_DNA_duplex_chain_A: CGCATGXTACGC
Cidofovir_DNA_duplex_chain_B: GCGTAGCATGCG

Data sets:
Data typeCount
13C chemical shifts4
1H chemical shifts162

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1Cidofovir DNA duplex, chain A1
2Cidofovir DNA duplex, chain B2

Entities:

Entity 1, Cidofovir DNA duplex, chain A 12 residues - Formula weight is not available

1   DCDGDCDADTDGL8PDTDADC
2   DGDC

Entity 2, Cidofovir DNA duplex, chain B 12 residues - Formula weight is not available

1   DGDCDGDTDADGDCDADTDG
2   DCDG

Samples:

sample_1: Cidofovir DNA duplex, chain_A 2 mM; Cidofovir DNA duplex, chain_B 2 mM; NaCl 50 mM; Na2HPO4 20 mM; EDTA 1 mM; DSS-d6 0.25 mM

sample_conditions_1: ionic strength: 70 mM; pH: 7.1; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D DQF-COSYsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1

Software:

VNMRJ v2.1B, Varian - collection

NMRPipe v4.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v8.0.b30, Johnson, One Moon Scientific - chemical shift assignment

MARDIGRAS, T.L. James - NOE calibration

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

CORMA, T.L. James - structure validation

NMR spectrometers:

  • Varian INOVA 600 MHz
  • Varian INOVA 500 MHz

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