Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
DNA/RNA HYBRID DUPLEX (5'-D(*GP*CP*TP*AP*TP*AP*APS*TP*GP*G)-3')(DOT) (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3') WITH A PHOSPHOROTHIOATE MOIETY
SOLUTION NMR
NMR Refinement
Method
Details
Software
molecular dynamics
NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 411 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0
AMBER4
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number
Conformers Submitted Total Number
1
Additional NMR Experimental Information
Details
THE PHOSPHATE BETWEEN NUCLEOTIDES SEVEN AND EIGHT IS MODIFIED BY SUBSTITUTING A SULFUR FOR ONE OF THE OXYGEN ATOMS. TWO SAMPLES WITH PURE CHIRALITY (R OR S) HAVE BEEN STUDIED; ONLY MINOR DIFFERENCES COULD BE DETECTED. THE COORDINATES REPRESENT THE S STEREOISOMER OF THE MODIFIED PHOSPHATE. THE SIXTH ROOT R-FACTOR, EXPRESSING THE FIT TO THE EXPERIMENTAL NOE DATA, CALCULATED WITH THE PROGRAM CORMA (KEEPERS AND JAMES), HAS A VALUE OF 0.074. THE ROOT MEAN SQUARE DEVIATION BETWEEN EXPERIMENTAL AND THEORETICAL DEOXYRIBOSE J-COUPLING CONSTRAINTS IS 2.01 HZ. THIS POOR FIT OF THE COUPLING CONSTANTS IS DUE TO CONFORMATIONAL FLEXIBILITY IN THE SUGAR RING.