2KH3
NMR Structure of Aflatoxin Formamidopyrimidine alpha-anomer in duplex DNA
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 1H-1H NOESY | 1 mM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE-1, 1 mM THYMIDINE-5'-MONOPHOSPHATE-2, 1 mM 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE-3, 1 mM Aflatoxin B1 Formamidopyrimidine-4, 1 mM 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE-5 | 100% D2O | 0.1 NaCl | 8.7 | 1 atm | 280 | |
| 2 | 1H-1H COSY | 1 mM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE-1, 1 mM THYMIDINE-5'-MONOPHOSPHATE-2, 1 mM 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE-3, 1 mM Aflatoxin B1 Formamidopyrimidine-4, 1 mM 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE-5 | 100% D2O | 0.1 NaCl | 8.7 | 1 atm | 280 | |
| 3 | 1H-1H NOESY | 1 mM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE-6, 1 mM THYMIDINE-5'-MONOPHOSPHATE-7, 1 mM 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE-8, 1 mM Aflatoxin B1 Formamidopyrimidine-9, 1 mM 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE-10 | 90% H2O/10% D2O | 0.1 NaCl | 8.7 | 1 atm | 280 | |
| 4 | 1H-31P COSY | 1 mM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE-1, 1 mM THYMIDINE-5'-MONOPHOSPHATE-2, 1 mM 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE-3, 1 mM Aflatoxin B1 Formamidopyrimidine-4, 1 mM 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE-5 | 100% D2O | 0.1 NaCl | 8.7 | 1 atm | 280 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| 2 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, molecular dynamics, simulated annealing and rMD refinement in explicit solvent | Amber | |
| NMR Ensemble Information | |
|---|---|
| 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 | refinement | Amber | 9 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm |
| 2 | chemical shift assignment | Sparky | Goddard | |
| 3 | data analysis | Sparky | Goddard | |
| 4 | processing | TopSpin | Bruker Biospin | |
| 5 | restraint generation | MARDIGRAS | Borgias, B.A. & James, T.L. | |
| 6 | structure validation | CORMA | James T.L. | |
| 7 | data analysis | Curves | Lavery, R. and Sklenar, H | |
