2N96 | pdb_00002n96

An unexpected mode of small molecule DNA binding provides the structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin A


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D DQF-COSY1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A100% D2O247.5ambient297
22D 1H-13C HSQC1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A100% D2O247.5ambient297
32D 1H-1H NOESY1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A100% D2O247.5ambient297
42D 1H-1H NOESY1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A100% D2O247.5ambient297
52D 1H-1H NOESY1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A90% H2O/10% D2O247.5ambient297
62D DQF-COSY1.1 uM DNA (5'-D(*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3)*(DG5)P*CP*TP*AP*TP*AP*GP*(DC3))-3'), 1.1 uM lomaiviticin A90% H2O/10% D2O247.5ambient297
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1AgilentDirect Drive800
NMR Refinement
MethodDetailsSoftware
molecular dynamicsAmber
NMR Ensemble Information
Conformer Selection Criteriastructures with the least restraint violations
Conformers Calculated Total Number1000
Conformers Submitted Total Number6
Representative Model1 (minimized average structure)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1structure calculationAmber14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman
2refinementAmber14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman