136D

SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES


SOLUTION NMR Experimental Data


NMR Refinement
Method RESTRAINED MOLECULAR DYNAMICS, DISTANCE GEOMETRY
Details RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ON IDEALIZED A'- AND B-FORM STARTING STRUCTURES. ONLY THE TRIPLEX REGION AND THE FIRST AND LAST RESIDUES OF EACH OF THE TWO LOOPS IN THE SEQUENCE WERE CONSIDERED. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SIX STRUCTURES WERE CALCULATED (THREE FROM EACH STARTING STRUCTURE) USING DISTANCE RESTRAINTS. IN THE SECOND STAGE, TWO OF THE SIX STRUCTURES WERE REFINED DIRECTLY AGAINST PRIMARY NOE DATA. THE R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT DURING THIS STAGE. THE FINAL R(1/6) VALUES FOR THE TWO AVERAGED MINIMIZED STRUCTURES WERE 0.04 AND 0.045. THE SUMMATION RUNS THROUGH ALL OBSERVED, QUANTIFIABLE CROSSPEAK INTENSITIES IN NOESY SPECTRA RECORDED AT MIXING TIMES OF 40, 90 AND 150 MS. RMSD BOND DISTANCES 0.016 ANGSTROMS RMSD BOND ANGLES 3.96 DEGREES RMS DEVIATIONS FROM IDEALIZED GEOMETRY FOR THE TWO AVERAGED MINIMIZED STRUCTURES ARE AS FOLLOWS: BOND (ANGSTROMS) 0.016 0.018 ANGLES (DEGREES) 3.959 4.212 IMPROPERS (DEGREES) 0.433 0.472
NMR Ensemble Information
Conformers Submitted Total Number 14
Additional NMR Experimental Information
1 STRUCTURE ANALYSES WERE CONDUCTED ON SIXTEEN STRUCTURES INCLUDING FOURTEEN STRUCTURES TAKEN FROM THE RESTRAINED MOLECULAR DYNAMICS TRAJECTORIES OF THE TWO REFINEMENTS, AND THE TWO AVERAGED MINIMIZED STRUCTURES. THE COORDINATES FOR THE TWO AVERAGED MINIMIZED STRUCTURES CAN BE FOUND IN PROTEIN DATA BANK ENTRIES 134D AND 135D, RESPECTIVELY. THE COORDINATES FOR THE 14 STRUCTURES FROM THE RESTRAINED MOLECULAR DYNAMICS TRAJECTORIES CAN BE FOUND IN ENTRY 136D.
Computation: NMR Software
# Classification Software Name Author
1 refinement X-PLOR BRUNGER