HEADER RNA 14-DEC-07 3BNQ TITLE CRYSTAL STRUCTURE OF THE HOMO SAPIENS MITOCHONDRIAL RIBOSOMAL DECODING TITLE 2 SITE IN THE PRESENCE OF SRCL2 (A1555G MUTANT, BR-DERIVATIVE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: A SITE OF HUMAN MITOCHONDRIAL RIBOSOME, A CHAIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: A SITE OF HUMAN MITOCHONDRIAL RIBOSOME, B CHAIN; COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS RIBOSOME, DECODING SITE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.KONDO,E.WESTHOF REVDAT 3 21-FEB-24 3BNQ 1 REMARK HETSYN LINK REVDAT 2 24-FEB-09 3BNQ 1 VERSN REVDAT 1 24-JUN-08 3BNQ 0 JRNL AUTH J.KONDO,E.WESTHOF JRNL TITL THE BACTERIAL AND MITOCHONDRIAL RIBOSOMAL A-SITE MOLECULAR JRNL TITL 2 SWITCHES POSSESS DIFFERENT CONFORMATIONAL SUBSTATES JRNL REF NUCLEIC ACIDS RES. V. 36 2654 2008 JRNL REFN ISSN 0305-1048 JRNL PMID 18346970 JRNL DOI 10.1093/NAR/GKN112 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.79 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) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 17514 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1728 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 1912 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.46700 REMARK 3 B22 (A**2) : 2.06200 REMARK 3 B33 (A**2) : -2.52800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -5.31000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : 0.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 65.27 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 : RNA_FREE.PARAM REMARK 3 PARAMETER FILE 2 : BRU.PARAM REMARK 3 PARAMETER FILE 3 : PAR2_XPLOR.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : SRO_XPLOR.PARAM REMARK 3 PARAMETER FILE 7 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 TOPOLOGY FILE 7 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BNQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000045742. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92070, 0.92110, 0.91625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17519 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 49.791 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : 0.37300 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE 2.12 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, KCL, SPERMINE REMARK 280 TETRACHLORIDE, PAROMOMYCIN, 2-METHYL-2,4-PENTANEDIOL, SRCL2, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 35.63300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.02800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.63300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.02800 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 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 SR SR A 201 LIES ON A SPECIAL POSITION. REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 U A 1 OP3 P OP1 OP2 REMARK 480 U B 1 OP3 P OP1 OP2 O5' REMARK 480 U C 1 OP3 P OP1 OP2 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 O2' A A 18 OP3 U B 1 2555 2.07 REMARK 500 REMARK 500 REMARK: NULL 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 U A 1 P U A 1 OP3 -0.087 REMARK 500 U B 1 P U B 1 OP3 -0.089 REMARK 500 U C 1 P U C 1 OP3 -0.087 REMARK 500 G D 1 P G D 1 OP3 -0.085 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 B 1 0.08 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 K C 301 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 10 O2 REMARK 620 2 HOH B 211 O 78.1 REMARK 620 3 C C 23 O2' 92.6 85.9 REMARK 620 4 C C 23 O2 157.8 122.3 81.2 REMARK 620 5 HOH D 231 O 93.0 95.9 174.4 93.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 301 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 23 O2' REMARK 620 2 C A 23 O2 79.5 REMARK 620 3 HOH B 224 O 174.9 95.5 REMARK 620 4 C C 10 O2 93.3 156.5 91.2 REMARK 620 5 HOH C 315 O 106.9 82.2 71.8 78.5 REMARK 620 6 HOH C 317 O 85.5 120.0 97.5 81.2 156.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR B 201 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 302 O REMARK 620 2 HOH B 203 O 89.8 REMARK 620 3 HOH B 204 O 89.9 179.5 REMARK 620 4 HOH B 205 O 89.7 90.1 89.5 REMARK 620 5 HOH B 206 O 90.0 90.2 90.2 179.6 REMARK 620 6 HOH B 207 O 179.1 90.6 89.7 91.1 89.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR B 202 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 303 O REMARK 620 2 HOH A 304 O 90.3 REMARK 620 3 HOH B 208 O 179.6 89.4 REMARK 620 4 HOH B 209 O 90.1 179.5 90.2 REMARK 620 5 HOH B 210 O 90.6 90.2 89.1 90.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR C 201 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 305 O REMARK 620 2 HOH C 306 O 90.1 REMARK 620 3 HOH C 307 O 89.8 90.0 REMARK 620 4 HOH D 209 O 179.7 89.9 89.8 REMARK 620 5 HOH D 210 O 89.7 89.7 179.5 90.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR C 202 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 309 O REMARK 620 2 HOH C 310 O 90.2 REMARK 620 3 HOH C 311 O 89.9 89.9 REMARK 620 4 HOH D 215 O 179.7 90.1 90.1 REMARK 620 5 HOH D 216 O 90.1 179.5 89.7 89.6 REMARK 620 6 HOH D 217 O 90.5 89.8 179.4 89.5 90.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR C 203 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 312 O REMARK 620 2 HOH C 313 O 90.4 REMARK 620 3 HOH C 314 O 90.0 89.9 REMARK 620 4 HOH D 218 O 179.7 89.8 89.8 REMARK 620 5 HOH D 219 O 89.9 179.7 90.1 89.9 REMARK 620 6 HOH D 220 O 89.8 89.7 179.5 90.4 90.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR D 201 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 304 O REMARK 620 2 HOH D 204 O 179.4 REMARK 620 3 HOH D 205 O 90.3 90.0 REMARK 620 4 HOH D 206 O 89.4 90.3 179.7 REMARK 620 5 HOH D 207 O 89.5 90.0 90.3 89.6 REMARK 620 6 HOH D 208 O 90.4 90.1 89.2 90.9 179.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR D 202 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 308 O REMARK 620 2 HOH D 203 O 90.3 REMARK 620 3 HOH D 211 O 179.6 90.1 REMARK 620 4 HOH D 212 O 89.9 179.7 89.6 REMARK 620 5 HOH D 213 O 90.3 90.2 89.6 89.6 REMARK 620 6 HOH D 214 O 89.9 90.0 90.2 90.1 179.7 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 PAR C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BNL RELATED DB: PDB REMARK 900 RELATED ID: 3BNN RELATED DB: PDB REMARK 900 RELATED ID: 3BNO RELATED DB: PDB REMARK 900 RELATED ID: 3BNP RELATED DB: PDB REMARK 900 RELATED ID: 3BNR RELATED DB: PDB REMARK 900 RELATED ID: 3BNS RELATED DB: PDB REMARK 900 RELATED ID: 3BNT RELATED DB: PDB DBREF 3BNQ A 1 23 PDB 3BNQ 3BNQ 1 23 DBREF 3BNQ B 1 23 PDB 3BNQ 3BNQ 1 23 DBREF 3BNQ C 1 23 PDB 3BNQ 3BNQ 1 23 DBREF 3BNQ D 1 21 PDB 3BNQ 3BNQ 1 21 SEQRES 1 A 23 U U G C G U C A C C 5BU C G SEQRES 2 A 23 A G C A A G U C G C SEQRES 1 B 23 U U G C G U C A C C 5BU C G SEQRES 2 B 23 A G C A A G U C G C SEQRES 1 C 23 U U G C G U C A C C 5BU C G SEQRES 2 C 23 A G C A A G U C G C SEQRES 1 D 21 G C G U C A C C 5BU C G A G SEQRES 2 D 21 C A A G U C G C MODRES 3BNQ 5BU A 11 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 3BNQ 5BU B 11 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 3BNQ 5BU C 11 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE MODRES 3BNQ 5BU D 9 U 5-BROMO-URIDINE-5'-MONOPHOSPHATE HET 5BU A 11 21 HET 5BU B 11 21 HET 5BU C 11 21 HET 5BU D 9 21 HET SR A 201 1 HET K A 301 1 HET SR B 201 1 HET SR B 202 1 HET PAR C 101 42 HET SR C 201 1 HET SR C 202 1 HET SR C 203 1 HET K C 301 1 HET SR D 201 1 HET SR D 202 1 HETNAM 5BU 5-BROMO-URIDINE-5'-MONOPHOSPHATE HETNAM SR STRONTIUM ION HETNAM K POTASSIUM ION HETNAM PAR PAROMOMYCIN HETSYN PAR PAROMOMYCIN I; AMMINOSIDIN; CATENULIN; CRESTOMYCIN; HETSYN 2 PAR MONOMYCIN A; NEOMYCIN E FORMUL 1 5BU 4(C9 H12 BR N2 O9 P) FORMUL 5 SR 8(SR 2+) FORMUL 6 K 2(K 1+) FORMUL 9 PAR C23 H45 N5 O14 FORMUL 16 HOH *133(H2 O) LINK O3' C A 10 P 5BU A 11 1555 1555 1.61 LINK O3' 5BU A 11 P C A 12 1555 1555 1.61 LINK O3' C B 10 P 5BU B 11 1555 1555 1.61 LINK O3' 5BU B 11 P C B 12 1555 1555 1.60 LINK O3' C C 10 P 5BU C 11 1555 1555 1.61 LINK O3' 5BU C 11 P C C 12 1555 1555 1.61 LINK O3' C D 8 P 5BU D 9 1555 1555 1.61 LINK O3' 5BU D 9 P C D 10 1555 1555 1.61 LINK O2 C A 10 K K C 301 1555 1555 2.95 LINK O2' C A 23 K K A 301 1555 1555 2.80 LINK O2 C A 23 K K A 301 1555 1555 2.85 LINK K K A 301 O HOH B 224 1555 1555 2.80 LINK K K A 301 O2 C C 10 1555 1555 2.90 LINK K K A 301 O HOH C 315 1555 1555 2.96 LINK K K A 301 O HOH C 317 1555 1555 2.88 LINK O HOH A 302 SR SR B 201 1555 1555 2.64 LINK O HOH A 303 SR SR B 202 1555 1555 2.64 LINK O HOH A 304 SR SR B 202 1555 1555 2.63 LINK SR SR B 201 O HOH B 203 1555 1555 2.63 LINK SR SR B 201 O HOH B 204 1555 1555 2.63 LINK SR SR B 201 O HOH B 205 1555 1555 2.63 LINK SR SR B 201 O HOH B 206 1555 1555 2.64 LINK SR SR B 201 O HOH B 207 1555 1555 2.63 LINK SR SR B 202 O HOH B 208 1555 1555 2.64 LINK SR SR B 202 O HOH B 209 1555 1555 2.64 LINK SR SR B 202 O HOH B 210 1555 1555 2.64 LINK O HOH B 211 K K C 301 1555 1555 2.87 LINK O2' C C 23 K K C 301 1555 1555 2.89 LINK O2 C C 23 K K C 301 1555 1555 2.78 LINK SR SR C 201 O HOH C 305 1555 1555 2.64 LINK SR SR C 201 O HOH C 306 1555 1555 2.64 LINK SR SR C 201 O HOH C 307 1555 1555 2.64 LINK SR SR C 201 O HOH D 209 1555 1555 2.64 LINK SR SR C 201 O HOH D 210 1555 1555 2.64 LINK SR SR C 202 O HOH C 309 1555 1555 2.64 LINK SR SR C 202 O HOH C 310 1555 1555 2.64 LINK SR SR C 202 O HOH C 311 1555 1555 2.64 LINK SR SR C 202 O HOH D 215 1555 1555 2.63 LINK SR SR C 202 O HOH D 216 1555 1555 2.64 LINK SR SR C 202 O HOH D 217 1555 1555 2.64 LINK SR SR C 203 O HOH C 312 1555 1555 2.64 LINK SR SR C 203 O HOH C 313 1555 1555 2.64 LINK SR SR C 203 O HOH C 314 1555 1555 2.64 LINK SR SR C 203 O HOH D 218 1555 1555 2.64 LINK SR SR C 203 O HOH D 219 1555 1555 2.64 LINK SR SR C 203 O HOH D 220 1555 1555 2.64 LINK K K C 301 O HOH D 231 1555 1555 2.88 LINK O HOH C 304 SR SR D 201 1555 1555 2.64 LINK O HOH C 308 SR SR D 202 1555 1555 2.64 LINK SR SR D 201 O HOH D 204 1555 1555 2.63 LINK SR SR D 201 O HOH D 205 1555 1555 2.63 LINK SR SR D 201 O HOH D 206 1555 1555 2.63 LINK SR SR D 201 O HOH D 207 1555 1555 2.63 LINK SR SR D 201 O HOH D 208 1555 1555 2.64 LINK SR SR D 202 O HOH D 203 1555 1555 2.64 LINK SR SR D 202 O HOH D 211 1555 1555 2.64 LINK SR SR D 202 O HOH D 212 1555 1555 2.64 LINK SR SR D 202 O HOH D 213 1555 1555 2.64 LINK SR SR D 202 O HOH D 214 1555 1555 2.64 SITE 1 AC1 3 HOH C 320 HOH C 321 HOH C 332 SITE 1 AC2 6 HOH A 302 HOH B 203 HOH B 204 HOH B 205 SITE 2 AC2 6 HOH B 206 HOH B 207 SITE 1 AC3 6 HOH C 304 HOH D 204 HOH D 205 HOH D 206 SITE 2 AC3 6 HOH D 207 HOH D 208 SITE 1 AC4 6 HOH A 331 HOH C 305 HOH C 306 HOH C 307 SITE 2 AC4 6 HOH D 209 HOH D 210 SITE 1 AC5 6 HOH A 303 HOH A 304 HOH B 208 HOH B 209 SITE 2 AC5 6 HOH B 210 HOH C 302 SITE 1 AC6 6 HOH C 308 HOH D 203 HOH D 211 HOH D 212 SITE 2 AC6 6 HOH D 213 HOH D 214 SITE 1 AC7 6 HOH C 309 HOH C 310 HOH C 311 HOH D 215 SITE 2 AC7 6 HOH D 216 HOH D 217 SITE 1 AC8 6 HOH C 312 HOH C 313 HOH C 314 HOH D 218 SITE 2 AC8 6 HOH D 219 HOH D 220 SITE 1 AC9 3 HOH A 306 HOH B 211 HOH D 231 SITE 1 BC1 3 HOH B 224 HOH C 315 HOH C 317 CRYST1 71.266 76.056 55.912 90.00 117.06 90.00 C 1 2 1 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 0.014032 0.000000 0.007168 0.00000 SCALE2 0.000000 0.013148 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020084 0.00000