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Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
10mM phosphate buffer; 100 mM NaCl
90% H2O/10% D2O
100 mM NaCl
6.8
ambient
273
2
2D NOESY
10mM phosphate buffer; 100 mM NaCl
100% D2O
100 mM NaCl
6.8
ambient
273
3
2D TOCSY
10mM phosphate buffer; 100 mM NaCl
100% D2O
100 mM NaCl
6.8
ambient
273
4
DQF-COSY
10mM phosphate buffer; 100 mM NaCl
100% D2O
100 mM NaCl
6.8
ambient
273
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
INOVA
600
NMR Refinement
Method
Details
Software
simulated annealing
molecular dynamics
the structures are based on a total of 531 restraints, 506 are NOE-derived
distance constraints, 25 dihedral angle restraints,40 distance restraints
from hydrogen bonds.
X-PLOR
NMR Ensemble Information
Conformer Selection Criteria
back calculated data agree with experimental NOESY spectrum
Conformers Calculated Total Number
10
Conformers Submitted Total Number
8
Representative Model
1 (lowest energy)
Additional NMR Experimental Information
Details
This structure was determined using standard methods for DNA-drug complex.