SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX
beta-D-Olivose; 2,6-dideoxy-beta-D-arabino-hexopyranose; 2,6-dideoxy-beta-D-glucopyranose; 2,6-dideoxy-beta-D-mannopyranose; 2-deoxy-beta-D-quinovopyranose; 2-deoxy-beta-D-rhamnoopyranose; D-Olivose; Olivose; 2,6-DIDEOXY-BETA-D-GLUCOSE; 2,6-DIDEOXY-BETA-D-MANNOSE
2,6-DIDEOXY-BETA-D-GALACTOSE; 2,6-DIDEOXY-BETA-D-TALOSE; 2,6-dideoxy-beta-D-lyxo-hexopyranose; 2-deoxy-beta-D-fucopyranose; 2,6-dideoxy-D-galactose; 2,6-dideoxy-galactose
2,6-DIDEOXY-3 C-METHYL-D-RIBOPYRANOSIDE; 2,6-dideoxy-3-C-methyl-beta-D-ribo-hexose; 2,6-dideoxy-3-C-methyl-D-ribo-hexose; 2,6-dideoxy-3-C-methyl-ribo-hexose
THE HYDROXYL PROTONS IN THE RELAXATION MATRIX REFINED STRUCTURES ARE NOT WELL DETERMINED. THE HYDROPHILIC SIDE CHAIN, THE B SUGAR RESIDUE DDA 1 AND DDA 7, AND RESIDUES T 1 AND C 2 ARE UNDETERMINED.
TWO STARTING MODELS WERE OBTAINED BY DOCKING THE MG2+ COORDINATED MITHRAMYCIN DIMER IN THE MINOR GROOVE OF A AND B FORM D(TCGCGA) DUPLEX. THESE MODELS WERE SUBSEQUENTLY REFINED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. THE TWO DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL TWO STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE R FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE TWO FINAL STRUCTURES ARE: MODEL 1 MODEL 2 R FACTOR 0.146 0.136 BOND (ANGSTROMS) 0.016 0.013 ANGLES (DEGREES) 3.410 3.369. THE STRUCTURE EXHIBITS APPROXIMATE TWO-FOLD SYMMETRY, PERPENDICULAR TO THE HELICAL AXIS AND PASSING THROUGH THE MAGNESIUM IN THE COMPLEX. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 1 WHEN APPLIED TO CHAIN A OF MODEL 1. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 2 WHEN APPLIED TO CHAIN A OF MODEL 2.