2LOA
Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D DQF-COSY | 0.6 mM DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3') | 100% D2O | 0.1 | 7.5 | ambient | 293 | |
| 2 | 2D 1H-1H TOCSY | 0.6 mM DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3') | 100% D2O | 0.1 | 7.5 | ambient | 293 | |
| 3 | 2D 1H-1H NOESY | 0.6 mM DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3') | 100% D2O | 0.1 | 7.5 | ambient | 293 | |
| 4 | 2D 1H-1H NOESY | 2.0 mM DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3') | 90% H2O/10% D2O | 0.1 | 7.5 | ambient | 278 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| DGSA-distance geometry simulated annealing, Docking with energy minimization | One of the structures from PDB 2lo8 was selected and used for docking of of the Zn(cy4q), One conformer was selected from the the cyana calculation above and the Zn(cy4q) docked using energy minimization and distance restraints obtained from NMR data. | CYANA |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with acceptable covalent geometry |
| Conformers Calculated Total Number | 1 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (most favorable docked structure) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | geometry optimization | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
| 2 | chemical shift assignment | Sparky | 3.14 | Goddard |
| 3 | data analysis | Sparky | 3.14 | Goddard |
| 4 | refinement | HyperChem | 6 | HyperCube, Inc |
| 5 | refinement | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
