| MOLECULAR DYNAMICS, MATRIX RELAXATION |
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. |
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