HEADER HYDROLASE 01-JUN-18 6GOB TITLE X-RAY STRUCTURE OF THE ADDUCT FORMED UPON REACTION OF LYSOZYME WITH A TITLE 2 PD(II) COMPLEX BEARING N,N-PYRIDYLBENZIMIDAZOLE DERIVATIVE WITH AN TITLE 3 ALKYLATED SULPHONATE SIDE CHAIN 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 PROTEIN-METALLODRUG INTERACTION, PALLADIUM-BASED DRUG, N- KEYWDS 2 PYRIDYLBENZIMIDAZOLE BIDENTATE LIGANDS, STACKING, NON COVALENT BOND, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MERLINO,G.FERRARO REVDAT 3 24-JAN-24 6GOB 1 SOURCE REMARK LINK ATOM REVDAT 2 08-AUG-18 6GOB 1 JRNL REVDAT 1 25-JUL-18 6GOB 0 JRNL AUTH G.FERRARO,A.M.MANSOUR,A.MERLINO JRNL TITL EXPLORING THE INTERACTIONS BETWEEN MODEL PROTEINS AND PD(II) JRNL TITL 2 OR PT(II) COMPOUNDS BEARING CHARGED N,N-PYRIDYLBENZIMIDAZOLE JRNL TITL 3 BIDENTATE LIGANDS BY X-RAY CRYSTALLOGRAPHY. JRNL REF DALTON TRANS V. 47 10130 2018 JRNL REFN ESSN 1477-9234 JRNL PMID 30004541 JRNL DOI 10.1039/C8DT01663A REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 8480 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 + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 434 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 578 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 33 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1001 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 143 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.33000 REMARK 3 B22 (A**2) : 0.33000 REMARK 3 B33 (A**2) : -0.66000 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): 0.235 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.188 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.136 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.886 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1266 ; 0.016 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1065 ; 0.010 ; 0.021 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1746 ; 2.215 ; 2.098 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2452 ; 1.862 ; 3.025 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 144 ; 6.194 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 56 ;32.725 ;22.321 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 185 ;16.137 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;18.534 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 160 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1465 ; 0.048 ; 0.023 REMARK 3 GENERAL PLANES OTHERS (A): 315 ; 0.003 ; 0.025 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL 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): 555 ; 1.684 ; 2.381 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 554 ; 1.684 ; 2.379 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 707 ; 2.355 ; 3.568 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 707 ; 2.346 ; 3.567 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 710 ; 2.623 ; 2.907 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 703 ; 2.499 ; 2.898 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1045 ; 4.057 ; 4.285 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1943 ; 5.822 ;28.807 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1942 ; 5.819 ;28.816 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 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6GOB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8938 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 56.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.50500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: 1DPX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% ETHYLENE GLYCOL 0.1 M SODIUM REMARK 280 ACETATE PH 4.4 0.6 M SODIUM NITRATE, VAPOR DIFFUSION, HANGING REMARK 280 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 18.65450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.74350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.74350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.98175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.74350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.74350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.32725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.74350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.74350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.98175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.74350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.74350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.32725 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 18.65450 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: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 350 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 422 LIES ON A SPECIAL POSITION. 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 F6Q A 209 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 ND1 REMARK 620 2 F6Q A 209 NAL 175.1 REMARK 620 3 F6Q A 209 NAQ 92.7 82.4 REMARK 620 4 F6Q A 209 CL2 85.2 99.7 177.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PD A 202 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 77 OD1 REMARK 620 2 HOH A 308 O 63.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PD A 201 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 87 OD2 REMARK 620 2 HOH A 373 O 172.8 REMARK 620 3 HOH A 393 O 90.7 93.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F6Q A 207 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 101 OD1 REMARK 620 2 F6Q A 207 NAL 125.3 REMARK 620 3 F6Q A 207 NAQ 136.2 72.2 REMARK 620 4 F6Q A 207 CL2 77.9 151.7 79.6 REMARK 620 5 ASP A 101 OD1 45.0 119.7 166.0 87.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 F6Q A 208 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 330 O REMARK 620 2 F6Q A 208 NAL 178.1 REMARK 620 3 F6Q A 208 NAQ 85.6 94.8 REMARK 620 4 HOH A 365 O 93.4 86.1 178.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PD A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F6Q A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F6Q A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F6Q A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F6Q A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F6Q A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 213 DBREF 6GOB 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 PD A 201 1 HET PD A 202 1 HET NO3 A 203 4 HET NO3 A 204 4 HET F6Q A 205 25 HET F6Q A 206 25 HET F6Q A 207 24 HET F6Q A 208 23 HET F6Q A 209 46 HET SO4 A 210 5 HET SO4 A 211 5 HET CL A 212 1 HET CL A 213 1 HETNAM PD PALLADIUM ION HETNAM NO3 NITRATE ION HETNAM F6Q N,N-PYRIDYLBENZIMIDAZOLE DERIVATIVE-PD COMPLEX HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 2 PD 2(PD 2+) FORMUL 4 NO3 2(N O3 1-) FORMUL 6 F6Q 5(C15 H15 CL2 N3 O3 PD S 2+) FORMUL 11 SO4 2(O4 S 2-) FORMUL 13 CL 2(CL 1-) FORMUL 15 HOH *150(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 ASP A 101 1 14 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 1.99 SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.04 SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.06 SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03 LINK ND1 HIS A 15 PD F6Q A 209 1555 1555 2.30 LINK OD1 ASN A 77 PD PD A 202 1555 1555 2.35 LINK OD2 ASP A 87 PD PD A 201 1555 1555 1.95 LINK OD1AASP A 101 PD F6Q A 207 1555 1555 2.69 LINK OD1BASP A 101 PD F6Q A 207 1555 1555 1.94 LINK PD PD A 201 O HOH A 373 1555 7555 2.09 LINK PD PD A 201 O HOH A 393 1555 1555 2.34 LINK PD PD A 202 O HOH A 308 1555 1555 2.33 LINK PD F6Q A 208 O HOH A 330 1555 1555 2.13 LINK PD F6Q A 208 O HOH A 365 1555 1555 2.35 SITE 1 AC1 6 ASP A 87 THR A 89 F6Q A 208 CL A 212 SITE 2 AC1 6 HOH A 373 HOH A 393 SITE 1 AC2 5 ASN A 77 F6Q A 208 CL A 213 HOH A 308 SITE 2 AC2 5 HOH A 365 SITE 1 AC3 10 CYS A 64 ASN A 65 ASP A 66 GLY A 67 SITE 2 AC3 10 ARG A 68 THR A 69 SER A 72 HOH A 305 SITE 3 AC3 10 HOH A 342 HOH A 435 SITE 1 AC4 4 ALA A 10 LYS A 13 ARG A 14 LEU A 129 SITE 1 AC5 10 ARG A 5 SER A 100 ASP A 101 ALA A 122 SITE 2 AC5 10 ARG A 125 GLY A 126 F6Q A 207 HOH A 322 SITE 3 AC5 10 HOH A 367 HOH A 375 SITE 1 AC6 13 TRP A 62 ASP A 101 GLY A 102 ASN A 103 SITE 2 AC6 13 GLY A 117 THR A 118 ASP A 119 GLN A 121 SITE 3 AC6 13 F6Q A 207 HOH A 302 HOH A 309 HOH A 326 SITE 4 AC6 13 HOH A 348 SITE 1 AC7 11 LYS A 33 ASN A 37 TRP A 62 TRP A 63 SITE 2 AC7 11 ARG A 73 LEU A 75 ASP A 101 GLY A 102 SITE 3 AC7 11 F6Q A 205 F6Q A 206 HOH A 381 SITE 1 AC8 12 LYS A 1 ASP A 87 PD A 201 PD A 202 SITE 2 AC8 12 CL A 212 HOH A 315 HOH A 330 HOH A 359 SITE 3 AC8 12 HOH A 365 HOH A 373 HOH A 383 HOH A 412 SITE 1 AC9 10 ARG A 14 HIS A 15 THR A 47 VAL A 92 SITE 2 AC9 10 ASN A 93 LYS A 96 ARG A 128 HOH A 301 SITE 3 AC9 10 HOH A 355 HOH A 421 SITE 1 AD1 7 LEU A 56 GLN A 57 ILE A 58 ASN A 59 SITE 2 AD1 7 TRP A 63 ALA A 107 TRP A 108 SITE 1 AD2 2 LYS A 116 GLY A 117 SITE 1 AD3 4 ASP A 87 PD A 201 F6Q A 208 HOH A 373 SITE 1 AD4 4 ASN A 77 PD A 202 HOH A 308 HOH A 441 CRYST1 79.487 79.487 37.309 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 0.012581 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012581 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026803 0.00000