207D

SOLUTION STRUCTURE OF MITHRAMYCIN DIMERS BOUND TO PARTIALLY OVERLAPPING SITES ON DNA


SOLUTION NMR
NMR Refinement
MethodDetailsSoftware
molecular dynamicsTWO STARTING STRUCTURES WERE OBTAINED BY MANUALLY DOCKING MITHRAMYCIN ON A FORM AND B FORM DNA. THESE WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCES DERIVED FROM NMR DATA (40, 80, 120, 160, 250 MS NOESY EXPERIMENTS) AND DELTA DIHEDRAL ANGLES DERIVED FROM SIMULATION OF COSY CROSS PEAK PATTERNS. THE EIGHT DISTANCE RESTRAINED STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 2.0 PS OF THE DYNAMICS DURING DISTANCE RESTRAINED DYNAMICS AND MINIMIZED. THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE EIGHT FINAL STRUCTURES ARE: BOND (ANG): MDL1 MDL2 MDL3 MDL4 MDL5 MDL6 MDL7 MDL8 0.009 0.009 0.009 0.008 0.009 0.009 0.009 0.009 ANGLE (DEG): MDL1 MDL2 MDL3 MDL4 MDL5 MDL6 MDL7 MDL8 2.627 2.630 2.631 2.636 2.621 2.638 2.664 2.652 IMPROPER(DEG): MDL1 MDL2 MDL3 MDL4 MDL5 MDL6 MDL7 MDL8 0.866 0.850 0.808 0.874 0.841 0.803 0.881 0.808X-PLOR
NMR Ensemble Information
Conformer Selection Criteriaall calculated structures submitted
Conformers Calculated Total Number8
Conformers Submitted Total Number8
Additional NMR Experimental Information
DetailsEACH MODEL CONTAINS FOUR MOLECULES OF MITHRAMYCIN (EACH WITH FORMULA C52 H75 O24, CHARGE -1) AND TWO MG++ CATIONS THAT COORDINATE TO TWO MITHRAMYCIN MOLECULES. IN THIS ENTRY MITHRAMYCIN IS PRESENTED AS HET GROUPS DDA-DDA-CHR- TSC. THE TSC RESIDUE IS COMPRISED OF THREE SACCHARIDE UNITS (DDA-DDL-MDA). THE HYDROPHILIC SIDE CHAIN AND THE A-B DISACCHARIDE OF MITHRAMYCIN MOLECULES ALONG WITH THE TERMINAL BASE PAIR IN THE DNA DUPLEX ARE NOT WELL DEFINED.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementX-PLORBRUNGER