PDB Short entry for 5Y87 HEADER RNA 19-AUG-17 5Y87 TITLE STRUCTURE-BASED INSIGHTS INTO SELF-CLEAVAGE BY A FOUR-WAY JUNCTIONAL TITLE 2 TWISTER-SISTER RIBOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(P*AP*CP*CP*CP*GP*CP*AP*AP*GP*GP*CP*CP*GP*AP*CP*GP*GP*C)-3'); COMPND 4 CHAIN: A, C; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA/RNA (50-MER); COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: METAGENOME; SOURCE 4 ORGANISM_TAXID: 256318; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: METAGENOME; SOURCE 8 ORGANISM_TAXID: 256318 KEYWDS TWISTER-SISTER, RIBOYZME, CATALYSIS, SELF-CLEAVING, RNA, MN2+ SOAKING EXPDTA X-RAY DIFFRACTION AUTHOR L.ZHENG,R.L.MICURA,A.REN REVDAT 3 27-MAR-24 5Y87 1 LINK REVDAT 2 23-JAN-19 5Y87 1 REMARK LINK SITE ATOM REVDAT 1 22-NOV-17 5Y87 0 JRNL AUTH L.ZHENG,E.MAIRHOFER,M.TEPLOVA,Y.ZHANG,J.MA,D.J.PATEL, JRNL AUTH 2 R.MICURA,A.REN JRNL TITL STRUCTURE-BASED INSIGHTS INTO SELF-CLEAVAGE BY A FOUR-WAY JRNL TITL 2 JUNCTIONAL TWISTER-SISTER RIBOZYME JRNL REF NAT COMMUN V. 8 1180 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 29081514 JRNL DOI 10.1038/S41467-017-01276-Y REMARK 2 REMARK 2 RESOLUTION. 2.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 44790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 2316 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 42.0814 - 5.4794 1.00 2515 124 0.1756 0.1879 REMARK 3 2 5.4794 - 4.3506 1.00 2511 131 0.1375 0.1934 REMARK 3 3 4.3506 - 3.8011 1.00 2469 141 0.1469 0.2118 REMARK 3 4 3.8011 - 3.4537 1.00 2467 175 0.1783 0.2027 REMARK 3 5 3.4537 - 3.2063 1.00 2523 131 0.1914 0.2558 REMARK 3 6 3.2063 - 3.0173 1.00 2489 140 0.2121 0.2746 REMARK 3 7 3.0173 - 2.8662 1.00 2535 119 0.2316 0.3001 REMARK 3 8 2.8662 - 2.7415 1.00 2493 143 0.2399 0.3127 REMARK 3 9 2.7415 - 2.6360 1.00 2468 136 0.2815 0.3443 REMARK 3 10 2.6360 - 2.5450 1.00 2517 152 0.2749 0.4226 REMARK 3 11 2.5450 - 2.4654 1.00 2487 119 0.2575 0.3423 REMARK 3 12 2.4654 - 2.3950 1.00 2551 130 0.2521 0.3611 REMARK 3 13 2.3950 - 2.3319 1.00 2427 142 0.2556 0.3520 REMARK 3 14 2.3319 - 2.2750 1.00 2575 131 0.2595 0.2789 REMARK 3 15 2.2750 - 2.2233 1.00 2480 139 0.2751 0.3395 REMARK 3 16 2.2233 - 2.1760 1.00 2476 126 0.2935 0.3655 REMARK 3 17 2.1760 - 2.1325 0.98 2491 137 0.3206 0.3778 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.005 3240 REMARK 3 ANGLE : 1.006 5044 REMARK 3 CHIRALITY : 0.042 678 REMARK 3 PLANARITY : 0.006 136 REMARK 3 DIHEDRAL : 11.449 1616 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: THE STRUCTURE FACTOR FILE CONTAINS REMARK 3 FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5Y87 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1300004826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.65 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44790 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.130 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NAOAC, PH 5.2, 0.15M CACL2, 18 REMARK 280 -22% MPD, 50-100MM MNCL2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 45.61050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.48150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 45.61050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.48150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 4260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 4050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 KCAL/MOL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OP1 A C 8 O HOH C 201 1.99 REMARK 500 O HOH D 307 O HOH D 328 2.03 REMARK 500 O HOH C 201 O HOH C 226 2.14 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 B 33 O5' - P - OP2 ANGL. DEV. = -5.9 DEGREES REMARK 500 A D 16 C8 - N9 - C4 ANGL. DEV. = 2.6 DEGREES 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 MN A 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 9 N7 REMARK 620 2 HOH A 201 O 111.1 REMARK 620 3 HOH A 211 O 92.0 156.6 REMARK 620 4 HOH B 224 O 173.8 74.9 82.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 108 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 202 O REMARK 620 2 HOH A 207 O 81.1 REMARK 620 3 HOH A 222 O 80.5 81.9 REMARK 620 4 G B 17 N7 95.3 93.0 173.9 REMARK 620 5 HOH B 290 O 94.8 175.4 95.5 89.2 REMARK 620 6 HOH B 293 O 161.9 90.3 82.5 101.1 93.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 210 O REMARK 620 2 HOH A 224 O 145.8 REMARK 620 3 HOH B 254 O 81.6 93.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 106 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 216 O REMARK 620 2 G B 41 O6 80.8 REMARK 620 3 HOH B 264 O 63.8 77.0 REMARK 620 4 HOH B 267 O 138.4 71.9 79.6 REMARK 620 5 HOH B 272 O 149.6 123.2 134.6 71.4 REMARK 620 6 HOH B 280 O 93.4 143.4 68.2 90.6 77.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 111 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 4 OP1 REMARK 620 2 HOH B 278 O 80.8 REMARK 620 3 C D 14 O2 82.3 135.3 REMARK 620 4 HOH D 221 O 101.0 69.2 73.9 REMARK 620 5 HOH D 283 O 93.3 75.0 147.2 138.5 REMARK 620 6 HOH D 287 O 85.6 141.8 76.9 148.8 70.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 107 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 7 OP1 REMARK 620 2 G B 38 OP1 100.9 REMARK 620 3 HOH B 220 O 87.6 87.8 REMARK 620 4 HOH B 246 O 171.7 87.0 90.3 REMARK 620 5 HOH B 255 O 100.9 98.0 168.5 80.1 REMARK 620 6 HOH B 274 O 86.5 165.5 80.1 85.2 92.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 102 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 42 OP2 REMARK 620 2 U B 43 OP2 88.8 REMARK 620 3 HOH B 217 O 89.1 98.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 103 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U B 43 OP1 REMARK 620 2 DC B 44 OP2 92.9 REMARK 620 3 HOH B 237 O 79.6 88.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 105 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 45 N1 REMARK 620 2 HOH B 284 O 73.1 REMARK 620 3 HOH D 223 O 148.5 79.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 104 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 47 N7 REMARK 620 2 HOH B 208 O 75.7 REMARK 620 3 HOH B 259 O 97.1 65.7 REMARK 620 4 HOH B 275 O 82.3 157.2 112.1 REMARK 620 5 HOH B 289 O 92.1 111.4 169.2 74.8 REMARK 620 6 HOH B 298 O 173.9 98.3 81.3 103.8 88.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 109 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 215 O REMARK 620 2 HOH B 219 O 91.8 REMARK 620 3 HOH B 222 O 80.9 169.7 REMARK 620 4 HOH B 252 O 88.8 94.7 77.9 REMARK 620 5 HOH B 294 O 170.4 88.3 97.6 81.5 REMARK 620 6 HOH B 295 O 95.6 94.5 93.6 169.7 94.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G C 9 N7 REMARK 620 2 HOH C 202 O 100.8 REMARK 620 3 HOH C 207 O 85.8 172.9 REMARK 620 4 HOH C 209 O 96.9 89.1 87.5 REMARK 620 5 HOH C 214 O 87.3 84.1 99.0 172.6 REMARK 620 6 HOH D 252 O 175.5 82.3 91.3 86.4 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 108 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 201 O REMARK 620 2 HOH C 204 O 93.5 REMARK 620 3 HOH C 226 O 49.1 79.8 REMARK 620 4 G D 17 N7 129.0 101.4 178.0 REMARK 620 5 HOH D 324 O 80.6 154.7 77.8 101.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 104 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 208 O REMARK 620 2 HOH C 213 O 57.7 REMARK 620 3 HOH C 229 O 143.6 89.9 REMARK 620 4 HOH D 206 O 84.0 114.1 96.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 103 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 211 O REMARK 620 2 G D 41 O6 78.9 REMARK 620 3 HOH D 227 O 87.5 84.3 REMARK 620 4 HOH D 269 O 70.7 83.7 156.8 REMARK 620 5 HOH D 305 O 144.1 80.7 119.5 77.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 102 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G D 7 OP1 REMARK 620 2 G D 38 OP1 96.6 REMARK 620 3 HOH D 235 O 92.0 90.9 REMARK 620 4 HOH D 284 O 174.9 88.4 89.2 REMARK 620 5 HOH D 291 O 94.8 95.9 169.7 83.3 REMARK 620 6 HOH D 314 O 87.8 171.5 81.6 87.4 91.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 105 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C D 42 OP2 REMARK 620 2 U D 43 OP2 84.2 REMARK 620 3 HOH D 207 O 84.5 100.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 106 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U D 43 OP1 REMARK 620 2 DC D 44 OP2 84.0 REMARK 620 3 HOH D 293 O 83.5 91.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 107 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G D 47 N7 REMARK 620 2 HOH D 244 O 80.5 REMARK 620 3 HOH D 295 O 74.5 73.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 208 O REMARK 620 2 HOH D 219 O 83.8 REMARK 620 3 HOH D 263 O 170.6 88.0 REMARK 620 4 HOH D 264 O 80.5 83.4 103.2 REMARK 620 5 HOH D 322 O 91.8 164.1 97.3 80.8 REMARK 620 6 HOH D 325 O 83.6 88.0 91.5 162.6 106.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 110 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 111 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN D 108 DBREF 5Y87 A 1 18 PDB 5Y87 5Y87 1 18 DBREF 5Y87 B 1 50 PDB 5Y87 5Y87 1 50 DBREF 5Y87 C 1 18 PDB 5Y87 5Y87 1 18 DBREF 5Y87 D 1 50 PDB 5Y87 5Y87 1 50 SEQRES 1 A 18 A C C C G C A A G G C C G SEQRES 2 A 18 A C G G C SEQRES 1 B 50 G C C G C C G C U G G U G SEQRES 2 B 50 C A A G U C C A G C C A C SEQRES 3 B 50 G C U U C G G C G U G G G SEQRES 4 B 50 C G C U DC A U G G G U SEQRES 1 C 18 A C C C G C A A G G C C G SEQRES 2 C 18 A C G G C SEQRES 1 D 50 G C C G C C G C U G G U G SEQRES 2 D 50 C A A G U C C A G C C A C SEQRES 3 D 50 G C U U C G G C G U G G G SEQRES 4 D 50 C G C U DC A U G G G U HET MN A 101 1 HET MN A 102 1 HET MN B 101 1 HET MN B 102 1 HET MN B 103 1 HET MN B 104 1 HET MN B 105 1 HET MN B 106 1 HET MN B 107 1 HET MN B 108 1 HET MN B 109 1 HET MN B 110 1 HET MN B 111 1 HET MN C 101 1 HET MN D 101 1 HET MN D 102 1 HET MN D 103 1 HET MN D 104 1 HET MN D 105 1 HET MN D 106 1 HET MN D 107 1 HET MN D 108 1 HETNAM MN MANGANESE (II) ION FORMUL 5 MN 22(MN 2+) FORMUL 27 HOH *286(H2 O) LINK N7 G A 9 MN MN A 101 1555 1555 2.56 LINK MN MN A 101 O HOH A 201 1555 1555 2.31 LINK MN MN A 101 O HOH A 211 1555 1555 2.48 LINK MN MN A 101 O HOH B 224 1555 1555 2.46 LINK O HOH A 202 MN MN B 108 1555 1555 2.34 LINK O HOH A 207 MN MN B 108 1555 1555 2.00 LINK O HOH A 210 MN MN B 101 1555 1555 2.69 LINK O HOH A 216 MN MN B 106 1555 1555 2.20 LINK O HOH A 222 MN MN B 108 1555 1555 2.35 LINK O HOH A 224 MN MN B 101 1555 1555 2.47 LINK OP1 G B 4 MN MN B 111 1555 1555 2.30 LINK OP1 G B 7 MN MN B 107 1555 1555 2.29 LINK N7 G B 17 MN MN B 108 1555 1555 2.40 LINK OP1 G B 38 MN MN B 107 1555 1555 2.03 LINK O6 G B 41 MN MN B 106 1555 1555 2.37 LINK OP2 C B 42 MN MN B 102 1555 1555 2.11 LINK OP2 U B 43 MN MN B 102 1555 1555 2.12 LINK OP1 U B 43 MN MN B 103 1555 1555 2.19 LINK OP2 DC B 44 MN MN B 103 1555 1555 2.28 LINK N1 A B 45 MN MN B 105 1555 1555 2.78 LINK N7 G B 47 MN MN B 104 1555 1555 2.36 LINK MN MN B 101 O HOH B 254 1555 1555 2.25 LINK MN MN B 102 O HOH B 217 1555 1555 2.51 LINK MN MN B 103 O HOH B 237 1555 1555 1.99 LINK MN MN B 104 O HOH B 208 1555 1555 2.41 LINK MN MN B 104 O HOH B 259 1555 1555 2.61 LINK MN MN B 104 O HOH B 275 1555 1555 2.66 LINK MN MN B 104 O HOH B 289 1555 1555 2.33 LINK MN MN B 104 O HOH B 298 1555 1555 2.49 LINK MN MN B 105 O HOH B 284 1555 1555 2.50 LINK MN MN B 105 O HOH D 223 1555 1555 2.18 LINK MN MN B 106 O HOH B 264 1555 1555 2.58 LINK MN MN B 106 O HOH B 267 1555 1555 2.62 LINK MN MN B 106 O HOH B 272 1555 1555 2.63 LINK MN MN B 106 O HOH B 280 1555 1555 2.54 LINK MN MN B 107 O HOH B 220 1555 1555 2.46 LINK MN MN B 107 O HOH B 246 1555 1555 1.97 LINK MN MN B 107 O HOH B 255 1555 1555 2.52 LINK MN MN B 107 O HOH B 274 1555 1555 2.07 LINK MN MN B 108 O HOH B 290 1555 1555 2.63 LINK MN MN B 108 O HOH B 293 1555 1555 2.51 LINK MN MN B 109 O HOH B 215 1555 1555 2.35 LINK MN MN B 109 O HOH B 219 1555 1555 2.60 LINK MN MN B 109 O HOH B 222 1555 1555 2.52 LINK MN MN B 109 O HOH B 252 1555 1555 2.15 LINK MN MN B 109 O HOH B 294 1555 1555 2.34 LINK MN MN B 109 O HOH B 295 1555 1555 2.12 LINK MN MN B 110 O HOH B 207 1555 1555 2.70 LINK MN MN B 111 O HOH B 278 1555 1555 2.38 LINK MN MN B 111 O2 C D 14 1555 1555 2.36 LINK MN MN B 111 O HOH D 221 1555 1555 2.59 LINK MN MN B 111 O HOH D 283 1555 1555 2.40 LINK MN MN B 111 O HOH D 287 1555 1555 2.58 LINK N7 G C 9 MN MN C 101 1555 1555 2.58 LINK MN MN C 101 O HOH C 202 1555 1555 2.37 LINK MN MN C 101 O HOH C 207 1555 1555 2.42 LINK MN MN C 101 O HOH C 209 1555 1555 2.31 LINK MN MN C 101 O HOH C 214 1555 1555 2.19 LINK MN MN C 101 O HOH D 252 1555 1555 2.34 LINK O HOH C 201 MN MN D 108 1555 1555 2.67 LINK O HOH C 204 MN MN D 108 1555 1555 2.27 LINK O HOH C 208 MN MN D 104 1555 1555 2.59 LINK O HOH C 211 MN MN D 103 1555 1555 2.28 LINK O HOH C 213 MN MN D 104 1555 1555 2.10 LINK O HOH C 226 MN MN D 108 1555 1555 2.46 LINK O HOH C 229 MN MN D 104 1555 1555 2.26 LINK OP1 G D 7 MN MN D 102 1555 1555 2.33 LINK N7 G D 17 MN MN D 108 1555 1555 2.40 LINK OP1 G D 38 MN MN D 102 1555 1555 2.06 LINK O6 G D 41 MN MN D 103 1555 1555 2.25 LINK OP2 C D 42 MN MN D 105 1555 1555 2.23 LINK OP2 U D 43 MN MN D 105 1555 1555 2.06 LINK OP1 U D 43 MN MN D 106 1555 1555 2.22 LINK OP2 DC D 44 MN MN D 106 1555 1555 2.40 LINK N7 G D 47 MN MN D 107 1555 1555 2.42 LINK MN MN D 101 O HOH D 208 1555 1555 2.43 LINK MN MN D 101 O HOH D 219 1555 1555 2.19 LINK MN MN D 101 O HOH D 263 1555 1555 2.43 LINK MN MN D 101 O HOH D 264 1555 1555 2.38 LINK MN MN D 101 O HOH D 322 1555 1555 2.36 LINK MN MN D 101 O HOH D 325 1555 1555 2.03 LINK MN MN D 102 O HOH D 235 1555 1555 2.41 LINK MN MN D 102 O HOH D 284 1555 1555 2.06 LINK MN MN D 102 O HOH D 291 1555 1555 2.42 LINK MN MN D 102 O HOH D 314 1555 1555 2.27 LINK MN MN D 103 O HOH D 227 1555 1555 2.44 LINK MN MN D 103 O HOH D 269 1555 1555 2.63 LINK MN MN D 103 O HOH D 305 1555 1555 2.42 LINK MN MN D 104 O HOH D 206 1555 1555 2.46 LINK MN MN D 105 O HOH D 207 1555 1555 2.56 LINK MN MN D 106 O HOH D 293 1555 1555 2.18 LINK MN MN D 107 O HOH D 244 1555 1555 2.00 LINK MN MN D 107 O HOH D 295 1555 1555 2.43 LINK MN MN D 108 O HOH D 324 1555 1555 2.45 SITE 1 AC1 4 G A 9 HOH A 201 HOH A 211 HOH B 224 SITE 1 AC2 3 HOH A 210 HOH A 224 HOH B 254 SITE 1 AC3 3 C B 42 U B 43 HOH B 217 SITE 1 AC4 3 U B 43 DC B 44 HOH B 237 SITE 1 AC5 6 G B 47 HOH B 208 HOH B 259 HOH B 275 SITE 2 AC5 6 HOH B 289 HOH B 298 SITE 1 AC6 4 C B 14 A B 45 HOH B 284 HOH D 223 SITE 1 AC7 6 HOH A 216 G B 41 HOH B 264 HOH B 267 SITE 2 AC7 6 HOH B 272 HOH B 280 SITE 1 AC8 6 G B 7 G B 38 HOH B 220 HOH B 246 SITE 2 AC8 6 HOH B 255 HOH B 274 SITE 1 AC9 6 HOH A 202 HOH A 207 HOH A 222 G B 17 SITE 2 AC9 6 HOH B 290 HOH B 293 SITE 1 AD1 6 HOH B 215 HOH B 219 HOH B 222 HOH B 252 SITE 2 AD1 6 HOH B 294 HOH B 295 SITE 1 AD2 1 HOH B 207 SITE 1 AD3 7 G B 4 HOH B 278 HOH C 227 C D 14 SITE 2 AD3 7 HOH D 221 HOH D 283 HOH D 287 SITE 1 AD4 6 G C 9 HOH C 202 HOH C 207 HOH C 209 SITE 2 AD4 6 HOH C 214 HOH D 252 SITE 1 AD5 6 HOH D 208 HOH D 219 HOH D 263 HOH D 264 SITE 2 AD5 6 HOH D 322 HOH D 325 SITE 1 AD6 6 G D 7 G D 38 HOH D 235 HOH D 284 SITE 2 AD6 6 HOH D 291 HOH D 314 SITE 1 AD7 5 HOH C 211 G D 41 HOH D 227 HOH D 269 SITE 2 AD7 5 HOH D 305 SITE 1 AD8 4 HOH C 208 HOH C 213 HOH C 229 HOH D 206 SITE 1 AD9 3 C D 42 U D 43 HOH D 207 SITE 1 AE1 3 U D 43 DC D 44 HOH D 293 SITE 1 AE2 4 G D 47 HOH D 244 HOH D 295 HOH D 330 SITE 1 AE3 5 HOH C 201 HOH C 204 HOH C 226 G D 17 SITE 2 AE3 5 HOH D 324 CRYST1 91.221 108.963 41.794 90.00 90.00 90.00 P 21 21 2 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 0.010962 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023927 0.00000