HEADER RNA 01-FEB-03 1NUV TITLE THE LEADZYME RIBOZYME BOUND TO MG(H2O)6(II) AND SR(II) AT 1.8 A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3'; COMPND 3 CHAIN: A, C, E, G; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3'; COMPND 7 CHAIN: B, D, F, H; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS RIBOZYME WAS MADE BY IN VITRO SELECTION, SOURCE 4 REPORTED BY PAN & UHLENBECK; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THIS RIBOZYME WAS MADE BY IN VITRO SELECTION, SOURCE 8 REPORTED BY PAN & UHLENBECK KEYWDS RIBOZYME, LEADZYME, LEAD-DEPENDENT CLEAVAGE, RNA, MG(H2O)6(II), KEYWDS 2 BULGED NUCLEOTIDES, HYDRATED MAGNESIUM, SR(II), PSEUDOHELICAL KEYWDS 3 PACKING, STICKY ENDS, ALTERNATE CONFORMATION, HOMOPURINE BASE PAIRS EXPDTA X-RAY DIFFRACTION AUTHOR J.E.WEDEKIND,D.B.MCKAY REVDAT 5 03-APR-24 1NUV 1 REMARK REVDAT 4 14-FEB-24 1NUV 1 REMARK LINK REVDAT 3 11-OCT-17 1NUV 1 REMARK REVDAT 2 24-FEB-09 1NUV 1 VERSN REVDAT 1 19-AUG-03 1NUV 0 JRNL AUTH J.E.WEDEKIND,D.B.MCKAY JRNL TITL CRYSTAL STRUCTURE OF THE LEADZYME AT 1.8 A RESOLUTION: METAL JRNL TITL 2 ION BINDING AND THE IMPLICATIONS FOR CATALYTIC MECHANISM AND JRNL TITL 3 ALLO SITE ION REGULATION. JRNL REF BIOCHEMISTRY V. 42 9554 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12911297 JRNL DOI 10.1021/BI0300783 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.E.WEDEKIND,D.B.MCKAY REMARK 1 TITL CRYSTAL STRUCTURE OF A LEAD DEPENDENT RIBOZYME REVEALING REMARK 1 TITL 2 METAL BINDING SITES RELEVANT TO CATALYSIS REMARK 1 REF NAT.STRUCT.BIOL. V. 6 261 1999 REMARK 1 REFN ISSN 1072-8368 REMARK 1 DOI 10.1038/6700 REMARK 2 REMARK 2 RESOLUTION. 1.81 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 23406 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) : 0.210 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1124 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1941 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 97 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 2048 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 407 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.29000 REMARK 3 B22 (A**2) : 4.29000 REMARK 3 B33 (A**2) : -8.59000 REMARK 3 B12 (A**2) : 0.33000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 43.38 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NUV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018227. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-99 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 : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI(311) REMARK 200 OPTICS : 16 POLE WIGGLER, FLAT MIRROR, REMARK 200 SI(311) BENT MONO WITH REMARK 200 HORIZONTAL FOCUS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24885 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 33.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.16400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 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: NDB ENTRY UR0001 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, MG-ACETATE, CACODYLATE, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. SOAKED IN 10 MM REMARK 280 SRCL2, PH 6.0, LIQUID DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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 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 44.36667 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 88.73333 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 66.55000 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 110.91667 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 22.18333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH C 148 O HOH H 276 6545 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 G C 24 O3' - P - OP2 ANGL. DEV. = 9.5 DEGREES REMARK 500 G C 24 O5' - P - OP1 ANGL. DEV. = -6.6 DEGREES REMARK 500 G G 26 O4' - C1' - N9 ANGL. DEV. = 4.5 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 G A 24 0.06 SIDE CHAIN REMARK 500 G A 26 0.07 SIDE CHAIN REMARK 500 G B 43 0.05 SIDE CHAIN REMARK 500 G C 26 0.06 SIDE CHAIN REMARK 500 G E 26 0.05 SIDE CHAIN REMARK 500 G G 24 0.06 SIDE CHAIN REMARK 500 G G 26 0.07 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 MG A 410 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 412 O REMARK 620 2 HOH A 413 O 95.9 REMARK 620 3 HOH A 414 O 103.1 160.6 REMARK 620 4 HOH A 415 O 96.6 82.8 90.6 REMARK 620 5 HOH A 416 O 166.8 74.2 87.7 90.9 REMARK 620 6 HOH B 425 O 97.4 91.5 90.4 165.4 74.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 411 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 417 O REMARK 620 2 HOH A 418 O 84.6 REMARK 620 3 HOH A 419 O 89.5 87.6 REMARK 620 4 HOH A 420 O 84.8 91.2 174.2 REMARK 620 5 HOH B 426 O 176.3 91.7 90.5 95.2 REMARK 620 6 HOH B 427 O 93.9 176.1 88.8 92.2 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 412 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 421 O REMARK 620 2 HOH A 422 O 81.4 REMARK 620 3 HOH A 423 O 94.9 101.6 REMARK 620 4 HOH B 428 O 88.3 168.0 85.4 REMARK 620 5 HOH B 429 O 172.5 96.0 92.6 93.4 REMARK 620 6 HOH B 430 O 82.9 99.0 158.6 73.3 90.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR B 424 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 456 O REMARK 620 2 HOH B 465 O 72.6 REMARK 620 3 HOH B 466 O 98.9 94.5 REMARK 620 4 HOH B 467 O 85.9 158.5 89.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR C 420 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C C 23 O2 REMARK 620 2 A C 25 OP1 118.1 REMARK 620 3 HOH C 147 O 88.7 115.6 REMARK 620 4 HOH C 157 O 71.7 76.2 160.3 REMARK 620 5 HOH C 325 O 120.0 80.8 136.6 58.0 REMARK 620 6 HOH C 395 O 152.4 80.6 64.1 135.3 81.1 REMARK 620 7 A D 45 N1 66.0 159.0 84.3 86.6 79.9 104.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 419 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 130 O REMARK 620 2 HOH C 136 O 90.3 REMARK 620 3 HOH D 158 O 82.6 157.9 REMARK 620 4 HOH D 348 O 153.1 102.4 76.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 418 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 151 O REMARK 620 2 HOH C 180 O 140.4 REMARK 620 3 HOH C 198 O 65.3 91.3 REMARK 620 4 HOH C 286 O 67.8 78.4 82.9 REMARK 620 5 HOH C 371 O 54.1 157.7 81.5 121.1 REMARK 620 6 HOH D 372 O 124.0 79.2 80.9 151.9 78.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR D 422 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 121 O REMARK 620 2 HOH D 123 O 86.6 REMARK 620 3 HOH D 192 O 88.8 72.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR E 421 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C E 23 O2 REMARK 620 2 A E 25 OP1 119.2 REMARK 620 3 HOH E 82 O 72.6 78.3 REMARK 620 4 HOH E 83 O 151.1 81.3 134.8 REMARK 620 5 HOH E 329 O 118.8 81.5 55.2 82.2 REMARK 620 6 A F 45 N1 67.6 159.7 86.4 100.7 78.8 REMARK 620 7 HOH F 114 O 82.1 120.7 153.9 69.5 139.1 78.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG E 416 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH E 90 O REMARK 620 2 HOH E 93 O 88.3 REMARK 620 3 HOH E 112 O 83.4 170.2 REMARK 620 4 HOH E 117 O 78.2 93.0 80.2 REMARK 620 5 HOH E 305 O 77.1 91.0 92.3 154.8 REMARK 620 6 HOH F 294 O 174.7 95.6 92.4 98.0 106.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG E 417 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH E 285 O REMARK 620 2 HOH E 287 O 71.0 REMARK 620 3 HOH E 302 O 87.9 79.4 REMARK 620 4 HOH E 367 O 78.8 81.7 159.7 REMARK 620 5 HOH E 370 O 164.9 95.6 82.7 106.7 REMARK 620 6 HOH F 293 O 86.5 154.0 87.1 107.2 104.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR F 425 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH F 330 O REMARK 620 2 HOH F 331 O 80.1 REMARK 620 3 HOH F 392 O 82.7 85.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG G 414 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH G 202 O REMARK 620 2 HOH G 203 O 78.5 REMARK 620 3 HOH G 205 O 88.4 86.2 REMARK 620 4 HOH G 206 O 86.4 92.9 174.9 REMARK 620 5 HOH H 201 O 172.5 94.2 89.8 95.4 REMARK 620 6 HOH H 204 O 100.8 175.1 89.0 91.9 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG G 413 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH G 222 O REMARK 620 2 HOH G 224 O 97.9 REMARK 620 3 HOH G 225 O 94.1 92.0 REMARK 620 4 HOH H 221 O 100.9 82.4 164.5 REMARK 620 5 HOH H 223 O 94.1 167.5 90.6 91.9 REMARK 620 6 HOH H 226 O 172.8 85.6 92.0 73.3 82.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG H 415 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH G 228 O REMARK 620 2 HOH G 229 O 83.3 REMARK 620 3 HOH G 231 O 96.9 91.0 REMARK 620 4 HOH H 227 O 92.7 174.3 85.4 REMARK 620 5 HOH H 230 O 174.7 93.7 87.4 90.6 REMARK 620 6 HOH H 232 O 86.2 102.4 166.4 81.3 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR H 423 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH G 284 O REMARK 620 2 HOH H 236 O 94.8 REMARK 620 3 HOH H 243 O 104.5 81.7 REMARK 620 4 HOH H 270 O 92.3 98.2 163.1 REMARK 620 5 HOH H 283 O 156.2 106.8 88.8 75.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG G 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG G 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG H 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR C 420 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR E 421 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR D 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR H 423 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR B 424 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR F 425 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: UR0001 RELATED DB: NDB REMARK 900 LEADZYME RIBOZYME REMARK 900 RELATED ID: 429D RELATED DB: PDB REMARK 900 LEADZYME 2.6 A RESOLUTION REMARK 900 RELATED ID: 1LDZ RELATED DB: PDB REMARK 900 LEADZYME BY NMR REMARK 900 RELATED ID: 2LDZ RELATED DB: PDB REMARK 900 LEADZYME BY NMR REMARK 900 RELATED ID: 1NUJ RELATED DB: PDB REMARK 900 REFINED LEADZYME STRUCTURE WITH 10 MM MG(II) DBREF 1NUV A 18 30 PDB 1NUV 1NUV 18 30 DBREF 1NUV B 39 49 PDB 1NUV 1NUV 39 49 DBREF 1NUV C 18 30 PDB 1NUV 1NUV 18 30 DBREF 1NUV D 39 49 PDB 1NUV 1NUV 39 49 DBREF 1NUV E 18 30 PDB 1NUV 1NUV 18 30 DBREF 1NUV F 39 49 PDB 1NUV 1NUV 39 49 DBREF 1NUV G 18 30 PDB 1NUV 1NUV 18 30 DBREF 1NUV H 39 49 PDB 1NUV 1NUV 39 49 SEQRES 1 A 13 C G G A C C G A G C C A G SEQRES 1 B 11 G C U G G G A G U C C SEQRES 1 C 13 C G G A C C G A G C C A G SEQRES 1 D 11 G C U G G G A G U C C SEQRES 1 E 13 C G G A C C G A G C C A G SEQRES 1 F 11 G C U G G G A G U C C SEQRES 1 G 13 C G G A C C G A G C C A G SEQRES 1 H 11 G C U G G G A G U C C HET MG A 410 1 HET MG A 411 1 HET MG B 412 1 HET SR B 424 1 HET MG C 418 1 HET MG C 419 1 HET SR C 420 1 HET SR D 422 1 HET MG E 416 1 HET MG E 417 1 HET SR E 421 1 HET SR F 425 1 HET MG G 413 1 HET MG G 414 1 HET MG H 415 1 HET SR H 423 1 HETNAM MG MAGNESIUM ION HETNAM SR STRONTIUM ION FORMUL 9 MG 10(MG 2+) FORMUL 12 SR 6(SR 2+) FORMUL 25 HOH *407(H2 O) LINK MG MG A 410 O HOH A 412 1555 1555 2.01 LINK MG MG A 410 O HOH A 413 1555 1555 2.02 LINK MG MG A 410 O HOH A 414 1555 1555 2.23 LINK MG MG A 410 O HOH A 415 1555 1555 2.04 LINK MG MG A 410 O HOH A 416 1555 1555 2.19 LINK MG MG A 410 O HOH B 425 1555 1555 2.20 LINK MG MG A 411 O HOH A 417 1555 1555 2.24 LINK MG MG A 411 O HOH A 418 1555 1555 2.16 LINK MG MG A 411 O HOH A 419 1555 1555 2.23 LINK MG MG A 411 O HOH A 420 1555 1555 2.15 LINK MG MG A 411 O HOH B 426 1555 1555 2.01 LINK MG MG A 411 O HOH B 427 1555 1555 2.28 LINK O HOH A 421 MG MG B 412 1555 1555 2.25 LINK O HOH A 422 MG MG B 412 1555 1555 1.99 LINK O HOH A 423 MG MG B 412 1555 1555 2.45 LINK MG MG B 412 O HOH B 428 1555 1555 2.35 LINK MG MG B 412 O HOH B 429 1555 1555 2.22 LINK MG MG B 412 O HOH B 430 1555 1555 2.14 LINK SR SR B 424 O HOH B 456 1555 1555 2.82 LINK SR SR B 424 O HOH B 465 1555 1555 2.34 LINK SR SR B 424 O HOH B 466 1555 1555 2.18 LINK SR SR B 424 O HOH B 467 1555 1555 2.20 LINK O2 C C 23 SR SR C 420 1555 1555 3.36 LINK OP1 A C 25 SR SR C 420 1555 1555 2.87 LINK O HOH C 130 MG MG C 419 1555 1555 2.47 LINK O HOH C 136 MG MG C 419 1555 1555 2.09 LINK O HOH C 147 SR SR C 420 1555 1555 2.67 LINK O HOH C 151 MG MG C 418 1555 1555 3.11 LINK O HOH C 157 SR SR C 420 1555 1555 2.28 LINK O HOH C 180 MG MG C 418 1555 1555 2.60 LINK O HOH C 198 MG MG C 418 1555 1555 2.38 LINK O HOH C 286 MG MG C 418 1555 1555 2.38 LINK O HOH C 325 SR SR C 420 1555 1555 2.83 LINK O HOH C 371 MG MG C 418 1555 1555 2.27 LINK O HOH C 395 SR SR C 420 1555 1555 3.00 LINK MG MG C 418 O HOH D 372 1555 1555 2.37 LINK MG MG C 419 O HOH D 158 1555 1555 2.67 LINK MG MG C 419 O HOH D 348 1555 1555 2.21 LINK SR SR C 420 N1 A D 45 1555 1555 2.85 LINK O HOH D 121 SR SR D 422 1555 1555 2.61 LINK O HOH D 123 SR SR D 422 1555 1555 2.33 LINK O HOH D 192 SR SR D 422 1555 1555 2.54 LINK O2 C E 23 SR SR E 421 1555 1555 3.39 LINK OP1 A E 25 SR SR E 421 1555 1555 2.85 LINK O HOH E 82 SR SR E 421 1555 1555 2.43 LINK O HOH E 83 SR SR E 421 1555 1555 3.06 LINK O HOH E 90 MG MG E 416 1555 1555 2.58 LINK O HOH E 93 MG MG E 416 1555 1555 2.22 LINK O HOH E 112 MG MG E 416 1555 1555 2.17 LINK O HOH E 117 MG MG E 416 1555 1555 2.47 LINK O HOH E 285 MG MG E 417 1555 1555 2.53 LINK O HOH E 287 MG MG E 417 1555 1555 2.49 LINK O HOH E 302 MG MG E 417 1555 1555 2.11 LINK O HOH E 305 MG MG E 416 1555 1555 2.23 LINK O HOH E 329 SR SR E 421 1555 1555 2.94 LINK O HOH E 367 MG MG E 417 1555 1555 2.28 LINK O HOH E 370 MG MG E 417 1555 1555 2.14 LINK MG MG E 416 O HOH F 294 1555 1555 2.09 LINK MG MG E 417 O HOH F 293 1555 1555 2.07 LINK SR SR E 421 N1 A F 45 1555 1555 2.84 LINK SR SR E 421 O HOH F 114 1555 1555 2.49 LINK O HOH F 330 SR SR F 425 1555 1555 2.32 LINK O HOH F 331 SR SR F 425 1555 1555 2.21 LINK O HOH F 392 SR SR F 425 1555 1555 2.42 LINK O HOH G 202 MG MG G 414 1555 1555 2.27 LINK O HOH G 203 MG MG G 414 1555 1555 2.15 LINK O HOH G 205 MG MG G 414 1555 1555 2.13 LINK O HOH G 206 MG MG G 414 1555 1555 2.08 LINK O HOH G 222 MG MG G 413 1555 1555 1.99 LINK O HOH G 224 MG MG G 413 1555 1555 2.23 LINK O HOH G 225 MG MG G 413 1555 1555 1.95 LINK O HOH G 228 MG MG H 415 1555 1555 2.21 LINK O HOH G 229 MG MG H 415 1555 1555 2.01 LINK O HOH G 231 MG MG H 415 1555 1555 2.20 LINK O HOH G 284 SR SR H 423 1555 1555 2.41 LINK MG MG G 413 O HOH H 221 1555 1555 2.26 LINK MG MG G 413 O HOH H 223 1555 1555 1.90 LINK MG MG G 413 O HOH H 226 1555 1555 2.22 LINK MG MG G 414 O HOH H 201 1555 1555 2.09 LINK MG MG G 414 O HOH H 204 1555 1555 2.26 LINK O HOH H 227 MG MG H 415 1555 1555 2.30 LINK O HOH H 230 MG MG H 415 1555 1555 2.15 LINK O HOH H 232 MG MG H 415 1555 1555 2.13 LINK O HOH H 236 SR SR H 423 1555 1555 2.13 LINK O HOH H 243 SR SR H 423 1555 1555 2.25 LINK O HOH H 270 SR SR H 423 1555 1555 2.29 LINK O HOH H 283 SR SR H 423 1555 1555 2.68 SITE 1 AC1 6 HOH A 412 HOH A 413 HOH A 414 HOH A 415 SITE 2 AC1 6 HOH A 416 HOH B 425 SITE 1 AC2 6 HOH A 417 HOH A 418 HOH A 419 HOH A 420 SITE 2 AC2 6 HOH B 426 HOH B 427 SITE 1 AC3 6 HOH A 421 HOH A 422 HOH A 423 HOH B 428 SITE 2 AC3 6 HOH B 429 HOH B 430 SITE 1 AC4 6 HOH G 222 HOH G 224 HOH G 225 HOH H 221 SITE 2 AC4 6 HOH H 223 HOH H 226 SITE 1 AC5 6 HOH G 202 HOH G 203 HOH G 205 HOH G 206 SITE 2 AC5 6 HOH H 201 HOH H 204 SITE 1 AC6 6 HOH G 228 HOH G 229 HOH G 231 HOH H 227 SITE 2 AC6 6 HOH H 230 HOH H 232 SITE 1 AC7 6 HOH E 90 HOH E 93 HOH E 112 HOH E 117 SITE 2 AC7 6 HOH E 305 HOH F 294 SITE 1 AC8 6 HOH E 285 HOH E 287 HOH E 302 HOH E 367 SITE 2 AC8 6 HOH E 370 HOH F 293 SITE 1 AC9 5 HOH C 180 HOH C 198 HOH C 286 HOH C 371 SITE 2 AC9 5 HOH D 372 SITE 1 BC1 4 HOH C 130 HOH C 136 HOH D 158 HOH D 348 SITE 1 BC2 7 C C 23 A C 25 HOH C 147 HOH C 157 SITE 2 BC2 7 HOH C 325 HOH C 395 A D 45 SITE 1 BC3 7 C E 23 A E 25 HOH E 82 HOH E 83 SITE 2 BC3 7 HOH E 329 A F 45 HOH F 114 SITE 1 BC4 3 HOH D 121 HOH D 123 HOH D 192 SITE 1 BC5 5 HOH G 284 HOH H 236 HOH H 243 HOH H 270 SITE 2 BC5 5 HOH H 283 SITE 1 BC6 4 HOH B 456 HOH B 465 HOH B 466 HOH B 467 SITE 1 BC7 3 HOH F 330 HOH F 331 HOH F 392 CRYST1 60.600 60.600 133.100 90.00 90.00 120.00 P 61 24 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 0.016502 0.009527 0.000000 0.00000 SCALE2 0.000000 0.019054 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007513 0.00000