HEADER RNA 20-MAR-07 2P7D TITLE A MINIMAL, 'HINGED' HAIRPIN RIBOZYME CONSTRUCT SOLVED WITH TITLE 2 MIMICS OF THE PRODUCT STRANDS AT 2.25 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5' SUBSTRATE STRAND, PENTAMERIC FRAGMENT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RIBOZYME STRAND I; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: DOMAIN-LINKING RESIDUE S9L AT THE 3'-END; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: RIBOZYME STRAND II; COMPND 12 CHAIN: C; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: DOMAIN-LINKING RESIDUE S9L AT THE 5'-END; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: RIBOZYME STRAND III; COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: CONTAINS THE S-TURN; COMPND 20 MOL_ID: 5; COMPND 21 MOLECULE: 3' SUBSTRATE STRAND, OCTAMERIC FRAGMENT; COMPND 22 CHAIN: P; COMPND 23 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE OCCURS NATURALLY IN TOBACCO SOURCE 4 RINGSPOT VIRUS SATELLITE RNA; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: SEQUENCE OCCURS NATURALLY IN TOBACCO SOURCE 8 RINGSPOT VIRUS SATELLITE RNA; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: SEQUENCE OCCURS NATURALLY IN TOBACCO SOURCE 12 RINGSPOT VIRUS SATELLITE RNA; SOURCE 13 MOL_ID: 4; SOURCE 14 SYNTHETIC: YES; SOURCE 15 OTHER_DETAILS: SEQUENCE OCCURS NATURALLY IN TOBACCO SOURCE 16 RINGSPOT VIRUS SATELLITE RNA; SOURCE 17 MOL_ID: 5; SOURCE 18 SYNTHETIC: YES; SOURCE 19 OTHER_DETAILS: SEQUENCE OCCURS NATURALLY IN TOBACCO SOURCE 20 RINGSPOT VIRUS SATELLITE RNA KEYWDS HAIRPIN RIBOZYME; PRODUCT MIMIC; TRANSITION-STATE KEYWDS 2 STABILIZATION; ACTIVE SITE WATERS; INDUCED FIT, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.T.TORELLI,J.KRUCINSKA,J.E.WEDEKIND REVDAT 3 24-FEB-09 2P7D 1 VERSN REVDAT 2 06-NOV-07 2P7D 1 JRNL REVDAT 1 22-MAY-07 2P7D 0 JRNL AUTH A.T.TORELLI,J.KRUCINSKA,J.E.WEDEKIND JRNL TITL A COMPARISON OF VANADATE TO A 2'-5' LINKAGE AT THE JRNL TITL 2 ACTIVE SITE OF A SMALL RIBOZYME SUGGESTS A ROLE JRNL TITL 3 FOR WATER IN TRANSITION-STATE STABILIZATION JRNL REF RNA V. 13 1052 2007 JRNL REFN ISSN 1355-8382 JRNL PMID 17488874 JRNL DOI 10.1261/RNA.510807 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.SALTER,J.KRUCINSKA,S.ALAM,V.GRUM-TOKARS, REMARK 1 AUTH 2 J.E.WEDEKIND REMARK 1 TITL WATER IN THE ACTIVE SITE OF AN ALL-RNA HAIRPIN REMARK 1 TITL 2 RIBOZYME AND EFFECTS OF GUA8 BASE VARIANTS ON THE REMARK 1 TITL 3 GEOMETRY OF PHOSPHORYL TRANSFER. REMARK 1 REF BIOCHEMISTRY V. 45 686 2006 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 16411744 REMARK 1 DOI 10.1021/BI051887K REMARK 1 REFERENCE 2 REMARK 1 AUTH S.ALAM,V.GRUM-TOKARS,J.KRUCINSKA,M.L.KUNDRACIK, REMARK 1 AUTH 2 J.E.WEDEKIND REMARK 1 TITL CONFORMATIONAL HETEROGENEITY AT POSITION U37 OF AN REMARK 1 TITL 2 ALL-RNA HAIRPIN RIBOZYME WITH IMPLICATIONS FOR REMARK 1 TITL 3 METAL BINDING AND THE CATALYTIC STRUCTURE OF THE REMARK 1 TITL 4 S-TURN. REMARK 1 REF BIOCHEMISTRY V. 44 14396 2005 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 16262240 REMARK 1 DOI 10.1021/BI051550I REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : PARKINSON ET AL. ACTA CRYST.D,52,57 (1996) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 948513.140 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 16605 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 811 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.39 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2535 REMARK 3 BIN R VALUE (WORKING SET) : 0.4540 REMARK 3 BIN FREE R VALUE : 0.4420 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 148 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1347 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 86.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.93000 REMARK 3 B22 (A**2) : -11.93000 REMARK 3 B33 (A**2) : 23.86000 REMARK 3 B12 (A**2) : -3.49000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.47 REMARK 3 ESD FROM SIGMAA (A) : 0.54 REMARK 3 LOW RESOLUTION CUTOFF (A) : 40.64 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.78 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 66.27 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : DNA-RNAATT REMARK 3 PARAMETER FILE 2 : COBALT.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : &_1_PARAMETER_INFILE_5 REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : DNA-RNAATT REMARK 3 TOPOLOGY FILE 2 : COBALT.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : &_1_TOPOLOGY_INFILE_5 REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2P7D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-07. REMARK 100 THE RCSB ID CODE IS RCSB042058. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : SIDE SCATTERING BENT CUBE- REMARK 200 ROOT I-BEAM SINGLE CRYSTAL; REMARK 200 ASYMMETRIC CUT 4.965 DEGS REMARK 200 OPTICS : FLAT MIRROR (VERTICAL REMARK 200 FOCUSING); SINGLE CRYSTAL REMARK 200 SI(111) BENT MONOCHROMATOR REMARK 200 (HORIZONTAL FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16622 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 40.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 7.240 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 23.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.95 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43400 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1ZFR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 250 MM LI2SO4, 2.5 MM [CO(NH3)6] REMARK 280 CL3, 2 MM SPERMIDINE-HCL, 20 MM NAF, 50 MM ASCORBIC ACID, 100 REMARK 280 MM SODIUM CACODYLATE BUFFER AND 18.5% PEG 2000 MME, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.80000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.60000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.20000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 112.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.40000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.80000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 89.60000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 112.00000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 67.20000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 22.40000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE RIBOZYME-SUBSTRATE COMPLEX IN THE ASYMMETRIC UNIT REMARK 300 ALSO REPRESENTS THE BIOLOGICAL UNIT REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, P REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 S9L B 14 O3P 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 U A 1 O4' - C1' - N1 ANGL. DEV. = -9.9 DEGREES REMARK 500 A A 5 N9 - C1' - C2' ANGL. DEV. = -14.1 DEGREES REMARK 500 A A 5 O4' - C1' - N9 ANGL. DEV. = 9.0 DEGREES REMARK 500 G B 8 N9 - C1' - C2' ANGL. DEV. = 8.4 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 U D 37 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 104 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 5 O3' REMARK 620 2 A A 5 O2' 54.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 103 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 104 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO D 101 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO B 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OUE RELATED DB: PDB REMARK 900 A RELATED MINIMAL, ALL-RNA HAIRPIN RIBOZYME CONSTRUCT REMARK 900 SOLVED TO 2.05 ANGSTROMS RESOLUTION WITH WATERS IDENTIFIED REMARK 900 IN THE ACTIVE SITE. REMARK 900 RELATED ID: 2P7D RELATED DB: PDB REMARK 900 RELATED ID: 2P7E RELATED DB: PDB REMARK 900 RELATED ID: 2P7F RELATED DB: PDB DBREF 2P7D A 1 5 PDB 2P7D 2P7D 1 5 DBREF 2P7D B 2 14 PDB 2P7D 2P7D 2 14 DBREF 2P7D C 15 31 PDB 2P7D 2P7D 15 31 DBREF 2P7D D 31 49 PDB 2P7D 2P7D 31 49 DBREF 2P7D P 6 13 PDB 2P7D 2P7D 6 13 SEQRES 1 A 5 U C C C A SEQRES 1 B 13 C G G U G A G A A G G G S9L SEQRES 1 C 17 G G C A G A G A A A C A C SEQRES 2 C 17 A C G A SEQRES 1 D 19 U C G U G G U A C A U U A SEQRES 2 D 19 C C U G C C SEQRES 1 P 8 G U C C A C C G HET S9L B 14 13 HET SO4 A 103 5 HET NA A 104 1 HET NCO D 101 7 HET NCO B 102 7 HETNAM S9L 2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL DIHYDROGEN HETNAM 2 S9L PHOSPHATE HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETNAM NCO COBALT HEXAMMINE(III) FORMUL 2 S9L C6 H15 O7 P FORMUL 6 SO4 O4 S 2- FORMUL 7 NA NA 1+ FORMUL 8 NCO 2(CO H18 N6 3+) FORMUL 10 HOH *37(H2 O) LINK O3' G B 13 P S9L B 14 1555 1555 1.61 LINK O3' S9L B 14 P G C 15 1555 1555 1.61 LINK O3' A A 5 NA NA A 104 1555 1555 2.87 LINK O2' A A 5 NA NA A 104 1555 1555 2.47 SITE 1 AC1 3 U A 1 C A 2 NCO B 102 SITE 1 AC2 2 A A 5 G B 8 SITE 1 AC3 4 A C 20 G C 21 A D 40 U D 41 SITE 1 AC4 6 C A 2 C A 3 SO4 A 103 G B 11 SITE 2 AC4 6 G B 12 G B 13 CRYST1 93.900 93.900 134.400 90.00 90.00 120.00 P 61 2 2 12 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 0.010650 0.006149 0.000000 0.00000 SCALE2 0.000000 0.012297 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007440 0.00000 MASTER 360 0 5 0 0 0 5 6 0 0 0 7 END