P1 HELIX NUCLEIC ACIDS (DNA/RNA) RIBONUCLEIC ACID
Structure of the P1 helix from group I self-splicing introns.
Divalent Metal Ion Binding to a Conserved Wobble Pair Defining the Upstream Site of Cleavage of Group I Self-Splicing Introns
GROUP I SELF-SPLICING INTRON, CONTAINING A UUCG TETRALOOP HAIRPIN AND A U(DOT)G WOBBLE PAIR WITHIN A DOUBLE HELIX
RNA (5'-R(*GP*GP*GP*AP*UP*AP*AP*CP*UP*UP*CP*GP*GP*UP*UP*GP*UP*CP*CP*C)-3')
THE RNA SAMPLE WAS OBTAINED BY IN VITRO TRANSCRIPTION USING THE T7 RNA POLYMERASE AND A DOUBLE STRANDED DNA TEMPLATE. THE RNA WAS THEN PURIFIED BY GEL ELECTROPHORESIS.
structures with the least restraint violations
NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 637 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 X-PLOR STANDARD BOND LENGTHS AND ANGLES. ANGLES IN THE SUGAR RING WERE MODIFIED ACCORDING TO THE VALUES FOUND IN "PRINCIPLE OF NUCLEIC ACID STRUCTURE" BY SAENGER. STARTING WITH 30 STRUCTURES WITH RANDOMIZED BACKBONE TORSION ANGLES, 20 STRUCTURES WERE FOUND TO HAVE CONVERGED AFTER A PERIOD OF SIMULATED ANNEALING WITH ONLY NOE-DERIVED (581) AND H-BOND CONSTRAINTS (20) FOLLOWED BY A PERIOD OF REFINEMENT WHERE 100 DIHEDRAL CONSTRAINTS DERIVED FROM J COUPLING ANALYSIS AND PHOSPHORUS CHEMICAL SHIFT VALUE WERE ADDED. NO DIHEDRAL ANGLE VIOLATIONS AND 0-2 NOE VIOLATIONS BETWEEN 0.1 - 0.3 ANGSTROMS WERE FOUND IN EACH OF THE 20 CONVERGED STRUCTURES.
RNA, DOUBLE HELIX, GROUP I, SELF-SPLICING INTRON, UUCG TETRALOOP HAIRPIN, WOBBLE PAIR