HEADER HYDROLASE 27-FEB-17 5NA9
TITLE THE X-RAY STRUCTURE OF BOVINE PANCREATIC RIBONUCLEASE INCUBATED IN THE
TITLE 2 PRESENCE OF AN EXCESS OF CARBOPLATIN (1:10 RATIO)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: RIBONUCLEASE PANCREATIC;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: RNASE 1,RNASE A;
COMPND 5 EC: 3.1.27.5
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS;
SOURCE 3 ORGANISM_COMMON: BOVINE;
SOURCE 4 ORGANISM_TAXID: 9913
KEYWDS CARBOPLATIN, RIBONUCLEASES, PROTEIN PLATINATION, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.FERRARO,A.MERLINO
REVDAT 2 17-JAN-24 5NA9 1 REMARK LINK
REVDAT 1 16-AUG-17 5NA9 0
JRNL AUTH D.PICONE,F.DONNARUMMA,G.FERRARO,G.GOTTE,A.FAGAGNINI,
JRNL AUTH 2 G.BUTERA,M.DONADELLI,A.MERLINO
JRNL TITL A COMPARISON STUDY ON RNASE A OLIGOMERIZATION INDUCED BY
JRNL TITL 2 CISPLATIN, CARBOPLATIN AND OXALIPLATIN.
JRNL REF J. INORG. BIOCHEM. V. 173 105 2017
JRNL REFN ISSN 1873-3344
JRNL PMID 28511060
JRNL DOI 10.1016/J.JINORGBIO.2017.05.005
REMARK 2
REMARK 2 RESOLUTION. 2.07 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0103
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) : 2.07
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.57
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 9157
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) : 0.182
REMARK 3 R VALUE (WORKING SET) : 0.178
REMARK 3 FREE R VALUE : 0.244
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 486
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) : 2.07
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12
REMARK 3 REFLECTION IN BIN (WORKING SET) : 648
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85
REMARK 3 BIN R VALUE (WORKING SET) : 0.1920
REMARK 3 BIN FREE R VALUE SET COUNT : 26
REMARK 3 BIN FREE R VALUE : 0.2510
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 948
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 17
REMARK 3 SOLVENT ATOMS : 215
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.52
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.14000
REMARK 3 B22 (A**2) : 0.14000
REMARK 3 B33 (A**2) : -0.46000
REMARK 3 B12 (A**2) : 0.07000
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): 0.196
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.185
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.748
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 983 ; 0.016 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 883 ; 0.006 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1331 ; 1.715 ; 1.930
REMARK 3 BOND ANGLES OTHERS (DEGREES): 2043 ; 1.039 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 125 ; 7.245 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 44 ;37.421 ;25.227
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 169 ;15.861 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;18.185 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 146 ; 0.100 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1138 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 226 ; 0.002 ; 0.020
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): 500 ; 1.901 ; 1.995
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 499 ; 1.900 ; 1.994
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 625 ; 3.124 ; 2.982
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 626 ; 3.122 ; 2.983
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 483 ; 2.544 ; 2.234
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 478 ; 2.245 ; 2.217
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 704 ; 3.794 ; 3.218
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1276 ; 7.190 ;18.080
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1151 ; 6.399 ;16.877
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 : NULL
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 5NA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-APR-17.
REMARK 100 THE DEPOSITION ID IS D_1200003761.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-JUL-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
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 MICROMAX-007
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : MIRRORS
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 : 9665
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070
REMARK 200 RESOLUTION RANGE LOW (A) : 55.570
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 4.700
REMARK 200 R MERGE (I) : 0.10900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 3.50
REMARK 200 R MERGE FOR SHELL (I) : 0.35500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200
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: 1RNX
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55.86
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE - 0.1 M SODIUM
REMARK 280 ACETATE PH 5.5 - 3.0 M CESIUM CHLORIDE, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-Z+2/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.84733
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.42367
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.42367
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.84733
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1990 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 7150 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -155.0 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 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 LYS A 104 CD CE NZ
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 O HOH A 377 O HOH A 430 2.02
REMARK 500 NZ LYS A 66 O HOH A 301 2.19
REMARK 500
REMARK 500 REMARK: NULL
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 HOH A 453 O HOH A 453 5557 1.98
REMARK 500 O HOH A 364 O HOH A 364 5557 2.07
REMARK 500 O HOH A 379 O HOH A 445 4747 2.13
REMARK 500 O HOH A 364 O HOH A 421 5557 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 HIS A 48 71.25 -102.72
REMARK 500 GLN A 60 -139.43 -102.14
REMARK 500 ASN A 94 75.85 -113.44
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 511 DISTANCE = 6.78 ANGSTROMS
REMARK 525 HOH A 512 DISTANCE = 7.35 ANGSTROMS
REMARK 525 HOH A 513 DISTANCE = 7.59 ANGSTROMS
REMARK 525 HOH A 514 DISTANCE = 8.15 ANGSTROMS
REMARK 525 HOH A 515 DISTANCE = 8.64 ANGSTROMS
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 CS A 205 CS
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER A 23 OG
REMARK 620 2 ASN A 24 OD1 85.1
REMARK 620 3 ASN A 113 O 76.9 59.5
REMARK 620 4 HOH A 314 O 101.1 140.0 160.5
REMARK 620 5 HOH A 347 O 105.7 103.3 51.1 112.6
REMARK 620 6 HOH A 463 O 65.1 146.4 97.0 65.4 72.5
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 QPT A 201 PT1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 MET A 29 SD
REMARK 620 2 QPT A 201 N2 165.5
REMARK 620 3 QPT A 201 N1 91.9 92.1
REMARK 620 4 QPT A 201 O2 87.7 88.4 179.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 QPT A 201 PT1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 MET A 29 SD
REMARK 620 2 QPT A 201 N2 89.1
REMARK 620 3 QPT A 201 N1 57.5 42.8
REMARK 620 4 QPT A 201 O2 96.5 44.6 80.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CS A 204 CS
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 31 O
REMARK 620 2 ASN A 34 OD1 69.4
REMARK 620 3 HOH A 337 O 141.7 103.4
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CS A 204 CS
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER A 32 O
REMARK 620 2 THR A 78 O 20.4
REMARK 620 3 HOH A 304 O 92.2 90.4
REMARK 620 4 HOH A 337 O 151.6 163.7 74.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CS A 202 CS
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 48 O
REMARK 620 2 GLU A 49 OE1 66.1
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CS A 203 CS
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASN A 62 OD1
REMARK 620 2 THR A 70 O 69.6
REMARK 620 3 TYR A 73 OH 89.5 94.1
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 QPT A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CS A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CS A 203
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CS A 204
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CS A 205
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 206
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 207
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 208
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 209
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 210
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 214
DBREF 5NA9 A 1 124 UNP P61823 RNAS1_BOVIN 27 150
SEQRES 1 A 124 LYS GLU THR ALA ALA ALA LYS PHE GLU ARG GLN HIS MET
SEQRES 2 A 124 ASP SER SER THR SER ALA ALA SER SER SER ASN TYR CYS
SEQRES 3 A 124 ASN GLN MET MET LYS SER ARG ASN LEU THR LYS ASP ARG
SEQRES 4 A 124 CYS LYS PRO VAL ASN THR PHE VAL HIS GLU SER LEU ALA
SEQRES 5 A 124 ASP VAL GLN ALA VAL CYS SER GLN LYS ASN VAL ALA CYS
SEQRES 6 A 124 LYS ASN GLY GLN THR ASN CYS TYR GLN SER TYR SER THR
SEQRES 7 A 124 MET SER ILE THR ASP CYS ARG GLU THR GLY SER SER LYS
SEQRES 8 A 124 TYR PRO ASN CYS ALA TYR LYS THR THR GLN ALA ASN LYS
SEQRES 9 A 124 HIS ILE ILE VAL ALA CYS GLU GLY ASN PRO TYR VAL PRO
SEQRES 10 A 124 VAL HIS PHE ASP ALA SER VAL
HET QPT A 201 7
HET CS A 202 1
HET CS A 203 1
HET CS A 204 2
HET CS A 205 1
HET CL A 206 1
HET CL A 207 1
HET CL A 208 1
HET CL A 209 1
HET CL A 210 1
HET CL A 211 1
HET CL A 212 1
HET CL A 213 1
HET CL A 214 1
HETNAM QPT CARBOPLATIN
HETNAM CS CESIUM ION
HETNAM CL CHLORIDE ION
FORMUL 2 QPT C6 H12 N2 O4 PT 2+
FORMUL 3 CS 4(CS 1+)
FORMUL 7 CL 9(CL 1-)
FORMUL 16 HOH *215(H2 O)
HELIX 1 AA1 THR A 3 MET A 13 1 11
HELIX 2 AA2 ASN A 24 ARG A 33 1 10
HELIX 3 AA3 SER A 50 VAL A 57 1 8
HELIX 4 AA4 CYS A 58 GLN A 60 5 3
SHEET 1 AA1 3 VAL A 43 VAL A 47 0
SHEET 2 AA1 3 MET A 79 GLU A 86 -1 O CYS A 84 N ASN A 44
SHEET 3 AA1 3 TYR A 97 LYS A 104 -1 O THR A 100 N ASP A 83
SHEET 1 AA2 4 LYS A 61 VAL A 63 0
SHEET 2 AA2 4 CYS A 72 GLN A 74 -1 O GLN A 74 N LYS A 61
SHEET 3 AA2 4 ILE A 106 GLU A 111 -1 O VAL A 108 N TYR A 73
SHEET 4 AA2 4 VAL A 116 SER A 123 -1 O ALA A 122 N ILE A 107
SSBOND 1 CYS A 26 CYS A 84 1555 1555 2.03
SSBOND 2 CYS A 40 CYS A 95 1555 1555 2.02
SSBOND 3 CYS A 58 CYS A 110 1555 1555 2.04
SSBOND 4 CYS A 65 CYS A 72 1555 1555 1.94
LINK OG SER A 23 CS CS A 205 1555 1555 3.10
LINK OD1 ASN A 24 CS CS A 205 1555 1555 3.21
LINK SD MET A 29 PT1 AQPT A 201 1555 1555 2.71
LINK SD MET A 29 PT1 BQPT A 201 1555 1555 2.59
LINK O LYS A 31 CS B CS A 204 1555 1555 3.22
LINK O SER A 32 CS A CS A 204 1555 1555 2.90
LINK OD1 ASN A 34 CS B CS A 204 1555 1555 3.07
LINK O HIS A 48 CS CS A 202 1555 1555 3.04
LINK OE1 GLU A 49 CS CS A 202 1555 1555 3.27
LINK OD1 ASN A 62 CS CS A 203 1555 1555 3.39
LINK O THR A 70 CS CS A 203 1555 1555 3.21
LINK OH TYR A 73 CS CS A 203 1555 1555 3.35
LINK O THR A 78 CS A CS A 204 1555 3865 2.89
LINK O ASN A 113 CS CS A 205 1555 4637 3.29
LINK CS A CS A 204 O HOH A 304 1555 2634 2.71
LINK CS A CS A 204 O HOH A 337 1555 2634 3.26
LINK CS B CS A 204 O HOH A 337 1555 2634 3.29
LINK CS CS A 205 O HOH A 314 1555 4747 3.27
LINK CS CS A 205 O HOH A 347 1555 1555 3.26
LINK CS CS A 205 O HOH A 463 1555 1555 3.50
CISPEP 1 TYR A 92 PRO A 93 0 14.38
CISPEP 2 ASN A 113 PRO A 114 0 -5.93
SITE 1 AC1 8 ASP A 14 SER A 16 THR A 17 TYR A 25
SITE 2 AC1 8 GLN A 28 MET A 29 SER A 32 ASP A 53
SITE 1 AC2 2 HIS A 48 GLU A 49
SITE 1 AC3 4 ASN A 62 THR A 70 TYR A 73 HOH A 340
SITE 1 AC4 5 LYS A 31 SER A 32 ASN A 34 THR A 78
SITE 2 AC4 5 HOH A 304
SITE 1 AC5 3 SER A 23 ASN A 24 ASN A 113
SITE 1 AC6 4 ARG A 10 ASN A 34 THR A 78 HOH A 481
SITE 1 AC7 3 THR A 3 HOH A 316 HOH A 463
SITE 1 AC8 1 SER A 15
SITE 1 AC9 3 LEU A 35 ARG A 39 HOH A 356
SITE 1 AD1 6 THR A 87 GLY A 88 SER A 90 LYS A 91
SITE 2 AD1 6 HOH A 386 HOH A 416
SITE 1 AD2 2 ASN A 24 ASN A 113
SITE 1 AD3 4 THR A 36 TYR A 92 PRO A 93 HOH A 327
SITE 1 AD4 3 PHE A 120 CL A 214 HOH A 355
SITE 1 AD5 4 HIS A 12 ASN A 44 THR A 45 CL A 213
CRYST1 64.168 64.168 64.271 90.00 90.00 120.00 P 32 2 1 6
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 0.015584 0.008997 0.000000 0.00000
SCALE2 0.000000 0.017995 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015559 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
