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Solution NMR structures of ATP-binding DNA aptamer in complex with ATP
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.8 mM DNA, 0.8 mM ATP, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium chloride, 0.02 mM DSS 99.96%D2O 70 mM 7 1 atm 293 Bruker AVANCE 600 4 2D 1H-1H NOESY 0.8 mM DNA, 0.8 mM ATP, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium chloride, 0.02 mM DSS 90% H2O/10% D2O 70 mM 7 1 atm 293 Bruker AVANCE 600 2 2D 1H-1H COSY 0.8 mM DNA, 0.8 mM ATP, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium chloride, 0.02 mM DSS 99.96%D2O 70 mM 7 1 atm 293 Bruker AVANCE 600 3 2D 1H-1H TOCSY 0.8 mM DNA, 0.8 mM ATP, 10 mM sodium phosphate, 50 mM sodium chloride, 10 mM magnesium chloride, 0.02 mM DSS 99.96%D2O 70 mM 7 1 atm 293 Bruker AVANCE 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600
NMR Refinement Method Details Software simulated annealing GROMACS energy minimization Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment TopSpin Bruker Biospin 2 structure calculation GROMACS GROMACS development team 3 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman