2MNX
Major groove orientation of the (2S)-N6-(2-hydroxy-3-buten-1-yl)-2'-deoxyadenosine DNA adduct induced by 1,2-epoxy-3-butene
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 0.51 mM 5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3', 0.51 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate pH 7.0 | 100% D2O | 0.100 | 7.0 | ambient | 288 | |
2 | 2D 1H-1H COSY | 0.51 mM 5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3', 0.51 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate pH 7.0 | 100% D2O | 0.100 | 7.0 | ambient | 288 | |
3 | 2D 1H-1H NOESY | 0.51 mM 5'-D(*CP*GP*GP*AP*CP*(6HB)P*AP*GP*AP*AP*G)-3', 0.51 mM 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3', 100 mM sodium chloride, 50 uM EDTA, 10 mM sodium phosphate pH 7.0 | 90% H2O/10% D2O | 0.100 | 7.0 | ambient | 283 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | TopSpin |
NMR Ensemble Information | |
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Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
Conformers Calculated Total Number | 9 |
Conformers Submitted Total Number | 9 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | Bruker Biospin | |
2 | processing | TopSpin | Bruker Biospin | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | peak picking | Sparky | Goddard | |
5 | data analysis | Sparky | Goddard | |
6 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
7 | structure solution | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
8 | data analysis | CORMA | James, T. L. | |
9 | conversion of intensities to distance restraints | MARDIGRAS | Brandan A. Borgias, T. L. James |