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 1N1N | pdb_00001n1n

Structure of Mispairing of the Deoxycytosine with Deoxyadenosine 5' to the 8,9-Dihydro-8-(N7-guanyl)-9-Hydroxy-Aflatoxin B1 Adduct


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESYthe sample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer for NMR containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2The sample was dissolved in 99.96% D2O.0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA7.2ambient278
2DQF-COSYthe sample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer for NMR containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2The sample was dissolved in 99.96% D2O.0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA7.2ambient278
3P-COSYthe sample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer for NMR containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2The sample was dissolved in 99.96% D2O.0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA7.2ambient278
42D NOESYthe sample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 6.7 for NMR studiesThe sample was dissolved in 99.96% D2O.0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA6.7ambient278
52D NOESYthe ample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2 for NMR studiesthe sample was dissolved in 9:1 H2O:D2O.0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA7.2ambient278
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE500
2BrukerAVANCE600
3BrukerAVANCE800
NMR Refinement
MethodDetailsSoftware
distance geometry simulated annealing NMR data : Felix 97, 2000 molecular dynamics : XPLOR, AMBER matrix relaxation CORMA torsion angle dynamics Gaussian 98, INSIGHTII (2000)Distance was calculated using RANDMARDI protocol from MARDIGRAS. The 20 structures obtained from molecular dynamics simulation using X-PLOR starting from random, and B-starting structures. The final structure emerged from average of 20 simulated annealing structure from B-form starting structure. The average structure was solvated using X-LEAP protocol in AMBER 6.0, and subjected to 1.4 ns MD simulation using AMBER 6.0 SANDER module, in presence of counter IONs. The final structure was obtained by energy minimization of simulated structure. Solvent, and counter ions were omitted. Back Calculations were performed using CORMA.X-PLOR
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number20
Conformers Submitted Total Number1
Representative Model1 (minimized average structure)
Additional NMR Experimental Information
DetailsThis structure was determined using standard 2D homonuclear techniques.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementX-PLOR6.5Brunger
2structure solutionInsight II2000Accelaris Inc
3data analysisFelix97, 2000Accelaris INC
4iterative matrix relaxationMARDIGRAS5.2, 6.2Borgias, B. A., & James, T. L.
5refinementAmber6.0Case
6collectionXwinNMR3Bruker Inc