HEADER PROTEIN BINDING 19-JUN-23 8PH7 TITLE X-RAY STRUCTURE OF THE ADDUCT FORMED UPON REACTION OF LYSOZYME WITH TITLE 2 [RU2CL(DPHF)(O2CCH3)3] IN CONDITION A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV; COMPND 5 EC: 3.2.1.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031 KEYWDS RUTHENIUM, PROTEIN INTERACTION, METALLODRUG, DIRUTHENIUM, HYDROLASE, KEYWDS 2 PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.TERAN,G.FERRARO,A.MERLINO REVDAT 3 23-OCT-24 8PH7 1 REMARK REVDAT 2 20-SEP-23 8PH7 1 JRNL REVDAT 1 13-SEP-23 8PH7 0 JRNL AUTH A.TERAN,G.FERRARO,P.IMBIMBO,A.E.SANCHEZ-PELAEZ,D.M.MONTI, JRNL AUTH 2 S.HERRERO,A.MERLINO JRNL TITL STERIC HINDRANCE AND CHARGE INFLUENCE ON THE CYTOTOXIC JRNL TITL 2 ACTIVITY AND PROTEIN BINDING PROPERTIES OF DIRUTHENIUM JRNL TITL 3 COMPLEXES. JRNL REF INT.J.BIOL.MACROMOL. V. 253 26666 2023 JRNL REFN ISSN 0141-8130 JRNL PMID 37660867 JRNL DOI 10.1016/J.IJBIOMAC.2023.126666 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0415 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 63.4 REMARK 3 NUMBER OF REFLECTIONS : 14799 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.017 REMARK 3 FREE R VALUE TEST SET COUNT : 742 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) : 1.41 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 104 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 6.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.5230 REMARK 3 BIN FREE R VALUE SET COUNT : 7 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1000 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29500 REMARK 3 B22 (A**2) : -0.29500 REMARK 3 B33 (A**2) : 0.58900 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.317 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1142 ; 0.009 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 986 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1550 ; 1.631 ; 1.700 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2247 ; 0.569 ; 1.597 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 136 ; 7.113 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 12 ; 8.498 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 172 ;15.923 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 148 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1462 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 302 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 213 ; 0.242 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 71 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 499 ; 0.166 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 43 ; 0.201 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.103 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 535 ; 2.250 ; 2.422 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 535 ; 2.247 ; 2.421 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 674 ; 3.464 ; 4.376 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 675 ; 3.467 ; 4.379 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 607 ; 3.067 ; 2.852 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 606 ; 3.067 ; 2.851 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 876 ; 4.998 ; 5.110 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 877 ; 4.995 ; 5.110 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8PH7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1292131316. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14799 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.406 REMARK 200 RESOLUTION RANGE LOW (A) : 54.921 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : 0.16400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.76400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 38.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M SUCCINIC ACID AT PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 19.14000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.83500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.83500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.71000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.83500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.83500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.57000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.83500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.83500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.71000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.83500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.83500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.57000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 19.14000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 HOH A 307 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 344 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 366 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 406 LIES ON A SPECIAL POSITION. 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 TRP A 123 CH2 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 LEU A 129 O LEU A 129 7554 2.07 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 ARG A 45 0.09 SIDE CHAIN REMARK 500 ARG A 128 0.11 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 ZWH A 203 RU1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 33 NZ REMARK 620 2 ZWH A 203 RU2 165.0 REMARK 620 3 ZWH A 203 N1 100.1 93.9 REMARK 620 4 ZWH A 203 O41 81.3 85.0 176.7 REMARK 620 5 ZWH A 203 O1 82.7 91.2 93.5 89.6 REMARK 620 6 ZWH A 203 O4 100.1 85.5 88.2 88.6 176.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 60 O REMARK 620 2 CYS A 64 O 80.4 REMARK 620 3 SER A 72 OG 102.8 168.5 REMARK 620 4 ARG A 73 O 98.4 86.7 103.6 REMARK 620 5 HOH A 326 O 171.1 108.4 68.3 84.2 REMARK 620 6 HOH A 368 O 91.3 87.4 81.5 167.6 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZQ2 A 201 RU2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD1 REMARK 620 2 ZQ2 A 201 O6 89.8 REMARK 620 3 ZQ2 A 201 RU1 71.6 92.5 REMARK 620 4 ZQ2 A 201 N2 95.7 174.3 88.1 REMARK 620 5 HOH A 305 O 91.9 82.0 162.7 99.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZQ2 A 201 RU1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD1 REMARK 620 2 ZQ2 A 201 O5 84.6 REMARK 620 3 ZQ2 A 201 RU2 50.3 85.3 REMARK 620 4 ZQ2 A 201 N1 89.6 174.1 92.1 REMARK 620 5 SIN A 202 O2 148.8 102.8 99.6 82.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZWH A 203 RU2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 303 O REMARK 620 2 ZWH A 203 N2 103.1 REMARK 620 3 ZWH A 203 O31 75.8 177.5 REMARK 620 4 ZWH A 203 O2 102.1 88.5 93.9 REMARK 620 5 ZWH A 203 O3 80.8 95.0 82.6 174.8 REMARK 620 6 ZWH A 203 RU1 165.9 87.7 93.1 87.1 89.2 REMARK 620 N 1 2 3 4 5 DBREF 8PH7 A 1 129 UNP P00698 LYSC_CHICK 19 147 SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU HET ZQ2 A 201 21 HET SIN A 202 8 HET ZWH A 203 37 HET NA A 204 1 HETNAM ZQ2 [RU2(N,N'-BIS(4-FLUOROPHENYL)FORMAMIDINATE)(1,1- HETNAM 2 ZQ2 ETHANEDIOL) HETNAM SIN SUCCINIC ACID HETNAM ZWH [RU2CL(N,N'-BIS(4-FLUOROPHENYL)FORMAMIDINATE)(1,1- HETNAM 2 ZWH ETHANEDIOL)(SUCCINIC ACID)2] HETNAM NA SODIUM ION HETSYN ZQ2 3-METHYL-6,8-DIPHENYL-2,4-DIOXA-6,8-DIAZA-1$L^{3}, HETSYN 2 ZQ2 5$L^{3}-DIRUTHENABICYCLO[3.3.0]OCTANE FORMUL 2 ZQ2 C15 H16 N2 O2 RU2 FORMUL 3 SIN C4 H6 O4 FORMUL 4 ZWH C23 H28 N2 O10 RU2 FORMUL 5 NA NA 1+ FORMUL 6 HOH *106(H2 O) HELIX 1 AA1 GLY A 4 HIS A 15 1 12 HELIX 2 AA2 ASN A 19 TYR A 23 5 5 HELIX 3 AA3 SER A 24 ASN A 37 1 14 HELIX 4 AA4 PRO A 79 SER A 85 5 7 HELIX 5 AA5 ILE A 88 SER A 100 1 13 HELIX 6 AA6 ASN A 103 ALA A 107 5 5 HELIX 7 AA7 TRP A 108 CYS A 115 1 8 HELIX 8 AA8 ASP A 119 ARG A 125 5 7 SHEET 1 AA1 3 THR A 43 ARG A 45 0 SHEET 2 AA1 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44 SHEET 3 AA1 3 ILE A 58 ASN A 59 -1 O ILE A 58 N TYR A 53 SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.02 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.10 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.12 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.00 LINK NZ LYS A 33 RU1 BZWH A 203 1555 1555 2.47 LINK O SER A 60 NA NA A 204 1555 1555 2.25 LINK O CYS A 64 NA NA A 204 1555 1555 2.68 LINK OG SER A 72 NA NA A 204 1555 1555 2.51 LINK O ARG A 73 NA NA A 204 1555 1555 2.61 LINK OD1 ASP A 101 RU2 AZQ2 A 201 1555 1555 2.09 LINK OD1 ASP A 101 RU1 AZQ2 A 201 1555 1555 2.58 LINK RU1 AZQ2 A 201 O2 SIN A 202 1555 1555 2.71 LINK RU2 AZQ2 A 201 O HOH A 305 1555 1555 2.62 LINK RU2 BZWH A 203 O HOH A 303 1555 1555 2.06 LINK NA NA A 204 O HOH A 326 1555 1555 2.38 LINK NA NA A 204 O HOH A 368 1555 1555 2.34 CRYST1 77.670 77.670 38.280 90.00 90.00 90.00 P 43 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 0.012875 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012875 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026123 0.00000