HEADER DNA, RNA 18-JUN-10 3NKB TITLE A 1.9A CRYSTAL STRUCTURE OF THE HDV RIBOZYME PRECLEAVAGE SUGGESTS BOTH TITLE 2 LEWIS ACID AND GENERAL ACID MECHANISMS CONTRIBUTE TO PHOSPHODIESTER TITLE 3 CLEAVAGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-D(*(DUR))-D(*GP*G)-R(P*CP*UP*UP*GP*CP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: THE HEPATITIS DELTA VIRUS RIBOZYME; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: NUCLEIC ACID WAS CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 SOURCE 10 RNA POLYMERASE KEYWDS CATALYTIC RNA, METAL-MEDIATED CATALYSIS, PHOSPHODIESTER CLEAVAGE, KEYWDS 2 DNA, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.-H.CHEN,R.YAJIMA,D.M.CHADALAVADA,E.CHASE,P.C.BEVILACQUA,B.L.GOLDEN REVDAT 2 06-SEP-23 3NKB 1 REMARK LINK REVDAT 1 01-SEP-10 3NKB 0 JRNL AUTH J.H.CHEN,R.YAJIMA,D.M.CHADALAVADA,E.CHASE,P.C.BEVILACQUA, JRNL AUTH 2 B.L.GOLDEN JRNL TITL A 1.9 A CRYSTAL STRUCTURE OF THE HDV RIBOZYME PRECLEAVAGE JRNL TITL 2 SUGGESTS BOTH LEWIS ACID AND GENERAL ACID MECHANISMS JRNL TITL 3 CONTRIBUTE TO PHOSPHODIESTER CLEAVAGE. JRNL REF BIOCHEMISTRY V. 49 6508 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20677830 JRNL DOI 10.1021/BI100670P REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6_289 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.110 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 19845 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1994 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.3633 - 4.1236 0.99 2017 249 0.1706 0.1881 REMARK 3 2 4.1236 - 3.2748 1.00 1969 234 0.1729 0.1994 REMARK 3 3 3.2748 - 2.8614 0.99 1984 203 0.2134 0.2478 REMARK 3 4 2.8614 - 2.6000 0.99 1957 196 0.2713 0.3187 REMARK 3 5 2.6000 - 2.4137 0.98 1866 228 0.2658 0.2883 REMARK 3 6 2.4137 - 2.2715 0.97 1907 209 0.2537 0.2880 REMARK 3 7 2.2715 - 2.1578 0.95 1830 206 0.2645 0.2950 REMARK 3 8 2.1578 - 2.0639 0.90 1763 183 0.2623 0.2961 REMARK 3 9 2.0639 - 1.9845 0.76 1474 169 0.2567 0.2985 REMARK 3 10 1.9845 - 1.9160 0.57 1084 117 0.2914 0.3145 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 36.69 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.62400 REMARK 3 B22 (A**2) : 3.82660 REMARK 3 B33 (A**2) : -4.45060 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 1719 REMARK 3 ANGLE : 1.254 2678 REMARK 3 CHIRALITY : 0.078 357 REMARK 3 PLANARITY : 0.005 72 REMARK 3 DIHEDRAL : 15.206 853 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NKB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059936. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20583 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 44.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.42300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1CX0 WITH PORTIONS OF P2 AND P4 DELETED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 MG/ML RNA, 10 MM MGCL2, 50 MM REMARK 280 POTASSIUM ACETATE, 1 MM SPERMINE, 30% MPD, PH 5.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.01000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.01000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 32.41850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.05350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.41850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.05350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.01000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.41850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.05350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.01000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.41850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 42.05350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 DUR A 1 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 DG A 2 P OP1 OP2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 G B 10 P G B 10 OP3 -0.124 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 B 208 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 24 OP1 REMARK 620 2 HOH B 596 O 87.1 REMARK 620 3 HOH B 604 O 103.9 97.4 REMARK 620 4 HOH B 645 O 94.6 168.0 93.7 REMARK 620 5 HOH B 647 O 168.4 99.6 84.7 76.9 REMARK 620 6 HOH B 657 O 79.3 80.4 176.1 88.2 92.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 209 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 25 O2 REMARK 620 2 HOH B 544 O 147.7 REMARK 620 3 HOH B 573 O 70.5 78.7 REMARK 620 4 HOH B 623 O 77.7 98.4 65.7 REMARK 620 5 HOH B 650 O 75.6 88.4 76.6 139.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 35 OP1 REMARK 620 2 HOH B 615 O 79.4 REMARK 620 3 HOH B 635 O 105.4 102.3 REMARK 620 4 HOH B 656 O 132.8 77.7 119.5 REMARK 620 5 HOH B 661 O 78.6 154.7 95.4 109.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 55 OP2 REMARK 620 2 U B 56 O4 92.6 REMARK 620 3 HOH B 507 O 81.4 77.8 REMARK 620 4 HOH B 508 O 88.6 96.9 168.4 REMARK 620 5 HOH B 509 O 166.7 84.3 85.3 104.5 REMARK 620 6 HOH B 516 O 91.4 159.8 83.2 103.1 87.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 205 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 57 OP2 REMARK 620 2 A B 58 OP2 80.0 REMARK 620 3 HOH B 502 O 82.4 150.6 REMARK 620 4 HOH B 504 O 72.5 78.3 74.0 REMARK 620 5 HOH B 506 O 102.7 110.5 96.3 169.4 REMARK 620 6 HOH B 543 O 154.2 93.2 92.4 81.8 103.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 207 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 64 OP1 REMARK 620 2 A B 65 OP2 66.0 REMARK 620 3 HOH B 600 O 61.9 73.8 REMARK 620 4 HOH B 613 O 78.7 80.8 139.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 570 O REMARK 620 2 HOH B 651 O 70.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 510 O REMARK 620 2 HOH B 511 O 95.2 REMARK 620 3 HOH B 513 O 173.0 79.3 REMARK 620 4 HOH B 514 O 90.2 86.2 85.2 REMARK 620 5 HOH B 515 O 93.4 89.2 90.9 174.4 REMARK 620 6 HOH B 555 O 98.3 166.3 87.1 91.5 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 206 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 524 O REMARK 620 2 HOH B 528 O 93.1 REMARK 620 3 HOH B 532 O 92.0 174.2 REMARK 620 4 HOH B 536 O 92.6 98.9 83.8 REMARK 620 5 HOH B 563 O 81.5 81.9 96.0 174.1 REMARK 620 6 HOH B 566 O 173.9 88.0 86.7 93.1 92.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 210 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 530 O REMARK 620 2 HOH B 630 O 67.0 REMARK 620 3 HOH B 631 O 124.6 85.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 210 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CX0 RELATED DB: PDB REMARK 900 HEPATITIS DELTA VIRUS RIBOZYME REMARK 900 RELATED ID: 1SJ3 RELATED DB: PDB REMARK 900 HEPATITIS DELTA VIRUS GEMONIC RIBOZYME PRECURSOR, WITH MG2+ BOUND DBREF 3NKB A 1 9 PDB 3NKB 3NKB 1 9 DBREF 3NKB B 10 73 PDB 3NKB 3NKB 10 73 SEQRES 1 A 9 DUR DG DG C U U G C A SEQRES 1 B 64 G G U C C G C A G C C U C SEQRES 2 B 64 C U C G C G G C G C A A G SEQRES 3 B 64 C U G G G C A A C A U U C SEQRES 4 B 64 C G A A A G G U A A U G G SEQRES 5 B 64 C G A A U G C G G A C C HET MG B 201 1 HET MG B 202 1 HET MG B 203 1 HET MG B 204 1 HET MG B 205 1 HET MG B 206 1 HET MG B 207 1 HET MG B 208 1 HET MG B 209 1 HET MG B 210 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 10(MG 2+) FORMUL 13 HOH *168(H2 O) LINK OP1 U B 24 MG MG B 208 1555 1555 2.24 LINK O2 C B 25 MG MG B 209 1555 1555 2.42 LINK OP1 G B 35 MG MG B 201 1555 1555 2.56 LINK OP2 G B 55 MG MG B 204 1555 1555 2.35 LINK O4 U B 56 MG MG B 204 1555 1555 2.34 LINK OP2 A B 57 MG MG B 205 1555 1555 2.29 LINK OP2 A B 58 MG MG B 205 1555 1555 2.20 LINK OP1 A B 64 MG MG B 207 1555 1555 2.62 LINK OP2 A B 65 MG MG B 207 1555 1555 2.77 LINK MG MG B 201 O HOH B 615 1555 1555 2.58 LINK MG MG B 201 O HOH B 635 1555 1555 2.63 LINK MG MG B 201 O HOH B 656 1555 1555 2.54 LINK MG MG B 201 O HOH B 661 1555 1555 2.38 LINK MG MG B 202 O HOH B 570 1555 1555 2.58 LINK MG MG B 202 O HOH B 651 1555 1555 2.71 LINK MG MG B 203 O HOH B 510 1555 1555 2.56 LINK MG MG B 203 O HOH B 511 1555 1555 2.41 LINK MG MG B 203 O HOH B 513 1555 1555 2.46 LINK MG MG B 203 O HOH B 514 1555 1555 2.35 LINK MG MG B 203 O HOH B 515 1555 1555 2.35 LINK MG MG B 203 O HOH B 555 1555 1555 2.36 LINK MG MG B 204 O HOH B 507 1555 1555 2.54 LINK MG MG B 204 O HOH B 508 1555 1555 2.53 LINK MG MG B 204 O HOH B 509 1555 1555 2.42 LINK MG MG B 204 O HOH B 516 1555 1555 2.50 LINK MG MG B 205 O HOH B 502 1555 1555 2.36 LINK MG MG B 205 O HOH B 504 1555 1555 2.55 LINK MG MG B 205 O HOH B 506 1555 1555 2.24 LINK MG MG B 205 O HOH B 543 1555 1555 2.31 LINK MG MG B 206 O HOH B 524 1555 1555 2.42 LINK MG MG B 206 O HOH B 528 1555 1555 2.39 LINK MG MG B 206 O HOH B 532 1555 1555 2.47 LINK MG MG B 206 O HOH B 536 1555 1555 2.39 LINK MG MG B 206 O HOH B 563 1555 1555 2.41 LINK MG MG B 206 O HOH B 566 1555 1555 2.40 LINK MG MG B 207 O HOH B 600 1555 1555 2.68 LINK MG MG B 207 O HOH B 613 1555 1555 2.69 LINK MG MG B 208 O HOH B 596 1555 1555 2.41 LINK MG MG B 208 O HOH B 604 1555 1555 2.41 LINK MG MG B 208 O HOH B 645 1555 1555 2.30 LINK MG MG B 208 O HOH B 647 1555 1555 2.35 LINK MG MG B 208 O HOH B 657 1555 1555 2.57 LINK MG MG B 209 O HOH B 544 1555 1555 1.89 LINK MG MG B 209 O HOH B 573 1555 1555 2.96 LINK MG MG B 209 O HOH B 623 1555 1555 2.05 LINK MG MG B 209 O HOH B 650 1555 1555 2.30 LINK MG MG B 210 O HOH B 530 1555 1555 2.86 LINK MG MG B 210 O HOH B 630 1555 1555 2.64 LINK MG MG B 210 O HOH B 631 1555 1555 2.79 SITE 1 AC1 7 G B 35 HOH B 522 HOH B 615 HOH B 635 SITE 2 AC1 7 HOH B 656 HOH B 661 HOH B 663 SITE 1 AC2 3 HOH B 570 HOH B 651 HOH B 653 SITE 1 AC3 6 HOH B 510 HOH B 511 HOH B 513 HOH B 514 SITE 2 AC3 6 HOH B 515 HOH B 555 SITE 1 AC4 6 G B 55 U B 56 HOH B 507 HOH B 508 SITE 2 AC4 6 HOH B 509 HOH B 516 SITE 1 AC5 7 U B 56 A B 57 A B 58 HOH B 502 SITE 2 AC5 7 HOH B 504 HOH B 506 HOH B 543 SITE 1 AC6 6 HOH B 524 HOH B 528 HOH B 532 HOH B 536 SITE 2 AC6 6 HOH B 563 HOH B 566 SITE 1 AC7 5 C B 32 A B 64 A B 65 HOH B 600 SITE 2 AC7 5 HOH B 613 SITE 1 AC8 6 U B 24 HOH B 596 HOH B 604 HOH B 645 SITE 2 AC8 6 HOH B 647 HOH B 657 SITE 1 AC9 5 C B 25 HOH B 544 HOH B 573 HOH B 623 SITE 2 AC9 5 HOH B 650 SITE 1 BC1 4 G B 40 HOH B 530 HOH B 630 HOH B 631 CRYST1 64.837 84.107 102.020 90.00 90.00 90.00 C 2 2 21 8 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 0.015423 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011890 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009802 0.00000