NMR Localization of Divalent Cations at the Active Site of the Neurospora VS Ribozyme Provides Insights Into RNA-Metal Ion Interactions
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 1 mM [U-100% 15N] RNA | 90% H2O/10% D2O | 5 mM Mg2+, 50 mM potassium chloride | 6.5 | ambient | 288 | |
| 2 | 2D 1H-15N HSQC NH2 only | 1 mM [U-100% 15N] RNA | 90% H2O/10% D2O | 5 mM Mg2+, 50 mM potassium chloride | 6.5 | ambient | 288 | |
| 3 | 2D 1H-13C HSQC | 0.9 mM [U-100% 13C; U-100% 15N] RNA | 100% D2O | 5 mM Mg2+, 50 mM potassium chloride | 6.5 | ambient | 298 | |
| 4 | 2D 1H-15N HSQC long-range | 0.9 mM [U-100% 13C; U-100% 15N] RNA | 90% H2O/10% D2O | 5 mM Mg2+, 50 mM potassium chloride | 6.5 | ambient | 288 | |
| 5 | 1D 31P | 0.2-0.4 mM phosphorothioate RNA | 90% H2O/10% D2O | 5 mM Mg2+/Cd2+, 50 mM potassium chloride | 6.5 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| 2 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | X-PLOR NIH | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 500 |
| Conformers Submitted Total Number | 21 |
| Representative Model | 1 (minimized average structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 2 | data analysis | NMRView | Johnson, One Moon Scientific | |
| 3 | data analysis | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 4 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
