1KVH

NCSi-gb-bulge-DNA complex induced formation of a DNA bulge structure by a molecular wedge ligand-post-activated neocarzinostatin chromophore

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 90% H2O, 10% D2O	90% H2O/10% D2O	0.1M NACL, 10 mM SODIUM PHOSPHATE	6.4		270
2	2D NOESY	ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 99.96% D2O	99.96% D2O	0.1M NACL, 10 mM SODIUM PHOSPHATE	6.4		278
3	DQF-COSY	ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 99.96% D2O	99.96% D2O	0.1M NACL, 10 mM SODIUM PHOSPHATE	6.4		278
4	PE-COSY	ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 99.96% D2O	99.96% D2O	0.1M NACL, 10 mM SODIUM PHOSPHATE	6.4		278
5	TOCSY, H-P COSY	ca. 1 mM NCSi-gb-bulge-DNA complex; 0.1 M NaCl, 10 mM sodium phosphate, and 0.1 mM EDTA buffer (pH 6.4); 99.96% D2O	99.96% D2O	0.1M NACL, 10 mM SODIUM PHOSPHATE	6.4		278

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AMX	600

NMR Refinement
Method	Details	Software
distance geometry (DG), restrained molecular dynamics (rMDS), and relaxation matrix refinement	A total of 681 NMR restraints is used to derive the final refined structures. The total restraints consist of 590 of NOE-derived distance restraints and 91 of dihedral angle restraints. Especially, 85 of intermolecular distance restraints are derived which represent the interaction between the drug and the bulge duplex.	X-PLOR

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted
Conformers Calculated Total Number	7
Conformers Submitted Total Number	7

Additional NMR Experimental Information
Details	This structure was determined using 2D homonuclear and heteronuclear techniques

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR	3.01	Brunger

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.