1HX4 | pdb_00001hx4

MOLECULAR TOPOLOGY OF POLYCYCLIC AROMATIC CARCINOGENS DETERMINES DNA ADDUCT CONFORMATION: A LINK TO TUMORIGENIC ACTIVITY

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1R-trans-anti-BPh (carcinogen) covalently bound to 11mer DNA duplex	aqueous solution	0.10	6.5	1 atm	277
2	P-COSY	1R-trans-anti-BPh (carcinogen) covalently bound to 11mer DNA duplex	aqueous solution	0.10	6.5	1 atm	277
3	1H-31P HSQC	1R-trans-anti-BPh (carcinogen) covalently bound to 11mer DNA duplex	aqueous solution	0.10	6.5	1 atm	277

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	INOVA	500
3	Varian	INOVA	400

NMR Refinement
Method	Details	Software
torsion angle dynamics, simulated annealing, relaxation matrix refinements, energe minimization	Nonexchangeable interproton distance restraints were obtained from the buildup of NOE cross peak volumes in NOESY data sets (55, 100, 150 and 200 ms mixing times) on the 1S-(-)-trans-anti-(BPh)GC and the 1R-(+)-trans-anti-(BPh)GC 11-mer DNA duplex adducts in D2O buffer at 23 and 18 sC, respectively, and bounds were set between 15% and 25% of the calculated distances using the fixed cytidine H5-H6 reference distance of 2.45 . Non-stereospecific assignments were treated with r-6 averaging. Interproton distance restraints involving exchangeable protons of the same complex were obtained from NOESY spectra (90 and 150 ms mixing times) in H2O buffer at 4 sC with bounds set between 20% and 25% of the calculated distance using the thymine imino to adenine H2 reference distance of 2.91 across an A*T base pair.	VNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	9
Conformers Submitted Total Number	9
Representative Model	1 (fewest violations)

Additional NMR Experimental Information
Details	D2O NMR experiments were performed at 13 degree C, H2O NMR experiments were performed at 4 degree C

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	VNMR	6.1	Varian Associates Inc.
2	data analysis	Felix	felix2000	MSI
3	refinement	X-PLOR	3.1	Brunger, A. T.

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.