HEADER DNA-RNA HYBRID 25-JUL-95 219D TITLE DNA/RNA HYBRID DUPLEX (5'-D(*GP*CP*TP*AP*TP*AP*APS*TP*GP*G)- TITLE 2 3')(DOT) (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3') WITH A TITLE 3 PHOSPHOROTHIOATE MOIETY COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PHOSPHOROTHIOATE LINK BETWEEN A 7 AND T 8; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: PHOSPHOROTHIOATE LINK BETWEEN A 7 AND T 8 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, RNA, NMR, HYBRID, PHOSPHOROTHIOATE, DNA/RNA COMPLEX, KEYWDS 2 DNA-RNA HYBRID EXPDTA SOLUTION NMR AUTHOR C.GONZALEZ,T.L.JAMES REVDAT 3 24-FEB-09 219D 1 VERSN REVDAT 2 01-APR-03 219D 1 JRNL REVDAT 1 15-OCT-95 219D 0 JRNL AUTH C.GONZALEZ,W.STEC,M.A.REYNOLDS,T.L.JAMES JRNL TITL STRUCTURE AND DYNAMICS OF A DNA.RNA HYBRID DUPLEX JRNL TITL 2 WITH A CHIRAL PHOSPHOROTHIOATE MOIETY: NMR AND JRNL TITL 3 MOLECULAR DYNAMICS WITH CONVENTIONAL AND JRNL TITL 4 TIME-AVERAGED RESTRAINTS. JRNL REF BIOCHEMISTRY V. 34 4969 1995 JRNL REFN ISSN 0006-2960 JRNL PMID 7711019 JRNL DOI 10.1021/BI00015A008 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.GONZALEZ,W.STEC,A.KOBYLANSKA,R.I.HOGREFE, REMARK 1 AUTH 2 M.A.REYNOLDS,T.L.JAMES REMARK 1 TITL STRUCTURAL STUDY OF A DNA(DOT)RNA HYBRID DUPLEX REMARK 1 TITL 2 WITH A CHIRAL PHOSPHOROTHIOATE MOIETY BY NMR: REMARK 1 TITL 3 EXTRACTION OF DISTANCE AND TORSION ANGLE REMARK 1 TITL 4 CONSTRAINTS AND IMINO PROTON EXCHANGE RATES REMARK 1 REF BIOCHEMISTRY V. 33 11062 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER4 REMARK 3 AUTHORS : PEARLMAN,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NUMBER OF ATOMS USED IN REFINEMENT. REMARK 3 NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 411 REMARK 3 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 REMARK 4 REMARK 4 219D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE PHOSPHATE BETWEEN NUCLEOTIDES SEVEN AND EIGHT IS REMARK 210 MODIFIED BY SUBSTITUTING A SULFUR FOR ONE OF THE OXYGEN ATOMS. REMARK 210 TWO SAMPLES WITH PURE CHIRALITY (R OR S) HAVE BEEN STUDIED; REMARK 210 ONLY MINOR DIFFERENCES COULD BE DETECTED. THE COORDINATES REMARK 210 REPRESENT THE S STEREOISOMER OF THE MODIFIED PHOSPHATE. THE REMARK 210 SIXTH ROOT R-FACTOR, EXPRESSING THE FIT TO THE EXPERIMENTAL REMARK 210 NOE DATA, CALCULATED WITH THE PROGRAM CORMA (KEEPERS AND REMARK 210 JAMES), HAS A VALUE OF 0.074. THE ROOT MEAN SQUARE DEVIATION REMARK 210 BETWEEN EXPERIMENTAL AND THEORETICAL DEOXYRIBOSE J-COUPLING REMARK 210 CONSTRAINTS IS 2.01 HZ. THIS POOR FIT OF THE COUPLING REMARK 210 CONSTANTS IS DUE TO CONFORMATIONAL FLEXIBILITY IN THE SUGAR REMARK 210 RING. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG A 1 C4' - C3' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DC A 2 O4' - C1' - C2' ANGL. DEV. = 3.2 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 3 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DA A 4 C3' - C2' - C1' ANGL. DEV. = 8.4 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA A 7 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 DA A 7 C4' - C3' - C2' ANGL. DEV. = -9.7 DEGREES REMARK 500 DA A 7 O4' - C1' - C2' ANGL. DEV. = -10.2 DEGREES REMARK 500 DA A 7 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 A B 13 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 U B 14 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 U B 15 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 A B 16 C3' - C2' - C1' ANGL. DEV. = 4.8 DEGREES REMARK 500 A B 16 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 U B 17 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 A B 18 C5' - C4' - O4' ANGL. DEV. = 5.7 DEGREES REMARK 500 A B 18 C3' - C2' - C1' ANGL. DEV. = 6.1 DEGREES REMARK 500 C B 20 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG A 1 0.07 SIDE_CHAIN REMARK 500 DA A 6 0.07 SIDE_CHAIN REMARK 500 DA A 7 0.07 SIDE_CHAIN REMARK 500 C B 11 0.09 SIDE_CHAIN REMARK 500 C B 12 0.07 SIDE_CHAIN REMARK 500 A B 13 0.11 SIDE_CHAIN REMARK 500 A B 18 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 219D A 1 10 PDB 219D 219D 1 10 DBREF 219D B 11 20 PDB 219D 219D 11 20 SEQRES 1 A 10 DG DC DT DA DT DA DA PST DG DG SEQRES 1 B 10 C C A U U A U A G C MODRES 219D PST A 8 DT THYMIDINE-5'-THIOPHOSPHATE HET PST A 8 20 HETNAM PST THYMIDINE-5'-THIOPHOSPHATE FORMUL 1 PST C10 H15 N2 O7 P S LINK O3' DA A 7 P PST A 8 1555 1555 1.60 LINK O3' PST A 8 P DG A 9 1555 1555 1.61 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MASTER 132 0 1 0 0 0 0 6 0 0 0 2 END