10 20 30 40 50 60 70 80 2P7D - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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