HEADER TRANSFERASE 11-JUL-16 5KT3
TITLE TERANRY COMPLEX OF HUMAN DNA POLYMERASE IOTA(26-445) INSERTING DCMPNPP
TITLE 2 OPPOSITE TEMPLATE G IN THE PRESENCE OF MN2+
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3');
COMPND 3 CHAIN: T;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3');
COMPND 7 CHAIN: P;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: DNA POLYMERASE IOTA;
COMPND 11 CHAIN: A;
COMPND 12 FRAGMENT: UNP RESIDUES 26-445;
COMPND 13 SYNONYM: ETA2,RAD30 HOMOLOG B;
COMPND 14 EC: 2.7.7.7;
COMPND 15 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 4 ORGANISM_TAXID: 32630;
SOURCE 5 MOL_ID: 2;
SOURCE 6 SYNTHETIC: YES;
SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 8 ORGANISM_TAXID: 32630;
SOURCE 9 MOL_ID: 3;
SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 11 ORGANISM_COMMON: HUMAN;
SOURCE 12 ORGANISM_TAXID: 9606;
SOURCE 13 GENE: POLI, RAD30B;
SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS DNA POLYMERASE, POLI, MANGANESE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.Y.CHOI,A.PATRA,M.YEOM,Y.S.LEE,Q.ZHANG,M.EGLI,F.P.GUENGERICH
REVDAT 6 06-MAR-24 5KT3 1 LINK
REVDAT 5 18-DEC-19 5KT3 1 REMARK
REVDAT 4 13-SEP-17 5KT3 1 JRNL REMARK
REVDAT 3 19-OCT-16 5KT3 1 JRNL
REVDAT 2 07-SEP-16 5KT3 1 JRNL
REVDAT 1 31-AUG-16 5KT3 0
JRNL AUTH J.Y.CHOI,A.PATRA,M.YEOM,Y.S.LEE,Q.ZHANG,M.EGLI,
JRNL AUTH 2 F.P.GUENGERICH
JRNL TITL KINETIC AND STRUCTURAL IMPACT OF METAL IONS AND GENETIC
JRNL TITL 2 VARIATIONS ON HUMAN DNA POLYMERASE IOTA.
JRNL REF J.BIOL.CHEM. V. 291 21063 2016
JRNL REFN ESSN 1083-351X
JRNL PMID 27555320
JRNL DOI 10.1074/JBC.M116.748285
REMARK 2
REMARK 2 RESOLUTION. 2.64 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.10.1_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) : 2.64
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.06
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 17652
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.207
REMARK 3 R VALUE (WORKING SET) : 0.204
REMARK 3 FREE R VALUE : 0.248
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120
REMARK 3 FREE R VALUE TEST SET COUNT : 904
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 44.0661 - 4.7896 1.00 2980 178 0.2001 0.2232
REMARK 3 2 4.7896 - 3.8024 1.00 2814 146 0.1855 0.2316
REMARK 3 3 3.8024 - 3.3219 1.00 2778 135 0.2015 0.2551
REMARK 3 4 3.3219 - 3.0183 1.00 2732 169 0.2172 0.2704
REMARK 3 5 3.0183 - 2.8020 1.00 2737 136 0.2441 0.3043
REMARK 3 6 2.8020 - 2.6368 1.00 2707 140 0.2254 0.2996
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) : 0.240
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.920
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 46.65
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.56
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 : 0.009 3390
REMARK 3 ANGLE : 1.024 4661
REMARK 3 CHIRALITY : 0.056 549
REMARK 3 PLANARITY : 0.007 539
REMARK 3 DIHEDRAL : 17.558 2023
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: NULL
REMARK 4
REMARK 4 5KT3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-16.
REMARK 100 THE DEPOSITION ID IS D_1000222698.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-OCT-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-F
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17727
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.640
REMARK 200 RESOLUTION RANGE LOW (A) : 44.060
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 21.20
REMARK 200 R MERGE (I) : 0.12400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.64
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 21.80
REMARK 200 R MERGE FOR SHELL (I) : 0.82900
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 (%): 56.88
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG MME 5000, 0.1M MES BUFFER,
REMARK 280 0.3M AMMONIUM SULFATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 277.15K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2
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 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
REMARK 290 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-Z+5/6
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 135.25800
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 67.62900
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.44350
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.81450
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 169.07250
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 135.25800
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 67.62900
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 33.81450
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 101.44350
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 169.07250
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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3980 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19700 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, 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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 26
REMARK 465 GLU A 27
REMARK 465 LEU A 28
REMARK 465 ALA A 29
REMARK 465 ASP A 30
REMARK 465 VAL A 31
REMARK 465 GLY A 32
REMARK 465 ALA A 33
REMARK 465 ALA A 34
REMARK 465 ALA A 35
REMARK 465 SER A 36
REMARK 465 SER A 37
REMARK 465 GLN A 38
REMARK 465 GLY A 39
REMARK 465 VAL A 40
REMARK 465 HIS A 41
REMARK 465 ASP A 42
REMARK 465 GLN A 43
REMARK 465 VAL A 44
REMARK 465 LEU A 45
REMARK 465 PRO A 46
REMARK 465 THR A 47
REMARK 465 PRO A 48
REMARK 465 ASN A 49
REMARK 465 ALA A 50
REMARK 465 SER A 375
REMARK 465 SER A 376
REMARK 465 GLU A 377
REMARK 465 LYS A 378
REMARK 465 HIS A 379
REMARK 465 TYR A 380
REMARK 465 GLY A 398
REMARK 465 THR A 399
REMARK 465 GLY A 400
REMARK 465 ASN A 401
REMARK 465 ALA A 440
REMARK 465 LEU A 441
REMARK 465 ASN A 442
REMARK 465 THR A 443
REMARK 465 ALA A 444
REMARK 465 LYS A 445
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 ARG A 126 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 163 CD CE NZ
REMARK 470 LYS A 270 CG CD CE NZ
REMARK 470 LYS A 296 CG CD CE NZ
REMARK 470 LYS A 334 CG CD CE NZ
REMARK 470 LYS A 335 CG CD CE NZ
REMARK 470 LYS A 363 CG CD CE NZ
REMARK 470 TYR A 374 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 GLN A 395 CG CD OE1 NE2
REMARK 470 LYS A 396 CG CD CE NZ
REMARK 470 TYR A 402 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 ASP A 410 CG OD1 OD2
REMARK 470 LYS A 414 CG CD CE NZ
REMARK 470 LYS A 423 CG CD CE NZ
REMARK 470 MET A 424 CG SD CE
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 637 O HOH A 655 1.99
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 DG T 842 O3' DG T 842 C3' -0.040
REMARK 500 DT T 847 O3' DT T 847 C3' -0.094
REMARK 500 GLU A 339 CB GLU A 339 CG -0.117
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 CYS A 62 57.92 29.92
REMARK 500 LYS A 85 -115.64 54.35
REMARK 500 ASN A 185 47.78 37.26
REMARK 500 LYS A 423 -27.33 -36.87
REMARK 500 CYS A 436 -167.52 -127.01
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 504 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DC P 872 OP1
REMARK 620 2 LYS A 262 O 175.5
REMARK 620 3 ILE A 267 O 86.5 91.3
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 503 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DC P 873 O3'
REMARK 620 2 ASP A 59 OD1 143.6
REMARK 620 3 ASP A 151 OD1 104.4 110.1
REMARK 620 4 GLU A 152 OE2 79.7 83.6 99.0
REMARK 620 5 0KX A 501 O2A 92.4 95.4 95.7 164.7
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 502 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 59 OD2
REMARK 620 2 LEU A 60 O 83.5
REMARK 620 3 ASP A 151 OD2 91.2 98.7
REMARK 620 4 0KX A 501 O1G 90.7 94.5 166.8
REMARK 620 5 0KX A 501 O2B 171.5 89.4 94.5 85.1
REMARK 620 6 0KX A 501 O2A 108.1 168.0 84.2 82.8 78.7
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 0KX A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 504
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5KT2 RELATED DB: PDB
REMARK 900 RELATED ID: 5KT4 RELATED DB: PDB
REMARK 900 RELATED ID: 5KT5 RELATED DB: PDB
REMARK 900 RELATED ID: 5KT6 RELATED DB: PDB
REMARK 900 RELATED ID: 5KT7 RELATED DB: PDB
DBREF 5KT3 T 838 847 PDB 5KT3 5KT3 838 847
DBREF 5KT3 P 867 873 PDB 5KT3 5KT3 867 873
DBREF 5KT3 A 26 445 UNP Q9UNA4 POLI_HUMAN 26 445
SEQRES 1 T 10 DC DT DG DG DG DG DT DC DC DT
SEQRES 1 P 7 DA DG DG DA DC DC DC
SEQRES 1 A 420 MET GLU LEU ALA ASP VAL GLY ALA ALA ALA SER SER GLN
SEQRES 2 A 420 GLY VAL HIS ASP GLN VAL LEU PRO THR PRO ASN ALA SER
SEQRES 3 A 420 SER ARG VAL ILE VAL HIS VAL ASP LEU ASP CYS PHE TYR
SEQRES 4 A 420 ALA GLN VAL GLU MET ILE SER ASN PRO GLU LEU LYS ASP
SEQRES 5 A 420 LYS PRO LEU GLY VAL GLN GLN LYS TYR LEU VAL VAL THR
SEQRES 6 A 420 CYS ASN TYR GLU ALA ARG LYS LEU GLY VAL LYS LYS LEU
SEQRES 7 A 420 MET ASN VAL ARG ASP ALA LYS GLU LYS CYS PRO GLN LEU
SEQRES 8 A 420 VAL LEU VAL ASN GLY GLU ASP LEU THR ARG TYR ARG GLU
SEQRES 9 A 420 MET SER TYR LYS VAL THR GLU LEU LEU GLU GLU PHE SER
SEQRES 10 A 420 PRO VAL VAL GLU ARG LEU GLY PHE ASP GLU ASN PHE VAL
SEQRES 11 A 420 ASP LEU THR GLU MET VAL GLU LYS ARG LEU GLN GLN LEU
SEQRES 12 A 420 GLN SER ASP GLU LEU SER ALA VAL THR VAL SER GLY HIS
SEQRES 13 A 420 VAL TYR ASN ASN GLN SER ILE ASN LEU LEU ASP VAL LEU
SEQRES 14 A 420 HIS ILE ARG LEU LEU VAL GLY SER GLN ILE ALA ALA GLU
SEQRES 15 A 420 MET ARG GLU ALA MET TYR ASN GLN LEU GLY LEU THR GLY
SEQRES 16 A 420 CYS ALA GLY VAL ALA SER ASN LYS LEU LEU ALA LYS LEU
SEQRES 17 A 420 VAL SER GLY VAL PHE LYS PRO ASN GLN GLN THR VAL LEU
SEQRES 18 A 420 LEU PRO GLU SER CYS GLN HIS LEU ILE HIS SER LEU ASN
SEQRES 19 A 420 HIS ILE LYS GLU ILE PRO GLY ILE GLY TYR LYS THR ALA
SEQRES 20 A 420 LYS CYS LEU GLU ALA LEU GLY ILE ASN SER VAL ARG ASP
SEQRES 21 A 420 LEU GLN THR PHE SER PRO LYS ILE LEU GLU LYS GLU LEU
SEQRES 22 A 420 GLY ILE SER VAL ALA GLN ARG ILE GLN LYS LEU SER PHE
SEQRES 23 A 420 GLY GLU ASP ASN SER PRO VAL ILE LEU SER GLY PRO PRO
SEQRES 24 A 420 GLN SER PHE SER GLU GLU ASP SER PHE LYS LYS CYS SER
SEQRES 25 A 420 SER GLU VAL GLU ALA LYS ASN LYS ILE GLU GLU LEU LEU
SEQRES 26 A 420 ALA SER LEU LEU ASN ARG VAL CYS GLN ASP GLY ARG LYS
SEQRES 27 A 420 PRO HIS THR VAL ARG LEU ILE ILE ARG ARG TYR SER SER
SEQRES 28 A 420 GLU LYS HIS TYR GLY ARG GLU SER ARG GLN CYS PRO ILE
SEQRES 29 A 420 PRO SER HIS VAL ILE GLN LYS LEU GLY THR GLY ASN TYR
SEQRES 30 A 420 ASP VAL MET THR PRO MET VAL ASP ILE LEU MET LYS LEU
SEQRES 31 A 420 PHE ARG ASN MET VAL ASN VAL LYS MET PRO PHE HIS LEU
SEQRES 32 A 420 THR LEU LEU SER VAL CYS PHE CYS ASN LEU LYS ALA LEU
SEQRES 33 A 420 ASN THR ALA LYS
HET 0KX A 501 28
HET MN A 502 1
HET MN A 503 1
HET MN A 504 1
HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
HETNAM MN MANGANESE (II) ION
FORMUL 4 0KX C9 H17 N4 O12 P3
FORMUL 5 MN 3(MN 2+)
FORMUL 8 HOH *65(H2 O)
HELIX 1 AA1 CYS A 62 ASN A 72 1 11
HELIX 2 AA2 PRO A 73 LYS A 76 5 4
HELIX 3 AA3 ASN A 92 LEU A 98 1 7
HELIX 4 AA4 VAL A 106 CYS A 113 1 8
HELIX 5 AA5 LEU A 124 SER A 142 1 19
HELIX 6 AA6 LEU A 157 LEU A 168 1 12
HELIX 7 AA7 GLN A 169 SER A 174 1 6
HELIX 8 AA8 ASN A 184 GLN A 186 5 3
HELIX 9 AA9 ASP A 192 GLY A 217 1 26
HELIX 10 AB1 ASN A 227 GLY A 236 1 10
HELIX 11 AB2 LEU A 247 GLU A 249 5 3
HELIX 12 AB3 SER A 250 SER A 257 1 8
HELIX 13 AB4 HIS A 260 ILE A 264 5 5
HELIX 14 AB5 GLY A 268 ALA A 277 1 10
HELIX 15 AB6 SER A 282 PHE A 289 1 8
HELIX 16 AB7 SER A 290 GLY A 299 1 10
HELIX 17 AB8 GLY A 299 PHE A 311 1 13
HELIX 18 AB9 SER A 338 GLY A 361 1 24
HELIX 19 AC1 PRO A 390 LEU A 397 1 8
HELIX 20 AC2 VAL A 404 VAL A 420 1 17
SHEET 1 AA1 6 VAL A 145 LEU A 148 0
SHEET 2 AA1 6 GLU A 152 ASP A 156 -1 O PHE A 154 N GLU A 146
SHEET 3 AA1 6 ILE A 55 LEU A 60 -1 N VAL A 58 O ASN A 153
SHEET 4 AA1 6 GLY A 220 ALA A 225 -1 O ALA A 225 N ILE A 55
SHEET 5 AA1 6 GLN A 243 VAL A 245 1 O THR A 244 N ALA A 222
SHEET 6 AA1 6 HIS A 181 VAL A 182 1 N HIS A 181 O GLN A 243
SHEET 1 AA2 4 MET A 104 ASN A 105 0
SHEET 2 AA2 4 LEU A 87 CYS A 91 -1 N VAL A 88 O MET A 104
SHEET 3 AA2 4 LEU A 80 GLN A 84 -1 N VAL A 82 O THR A 90
SHEET 4 AA2 4 VAL A 117 ASN A 120 1 O VAL A 117 N GLY A 81
SHEET 1 AA3 4 SER A 326 CYS A 336 0
SHEET 2 AA3 4 LEU A 428 LYS A 439 -1 O PHE A 435 N PHE A 327
SHEET 3 AA3 4 LYS A 363 ARG A 373 -1 N ILE A 370 O SER A 432
SHEET 4 AA3 4 ARG A 382 PRO A 388 -1 O ARG A 385 N LEU A 369
LINK OP1 DC P 872 MN MN A 504 1555 1555 2.62
LINK O3' DC P 873 MN MN A 503 1555 1555 2.23
LINK OD2 ASP A 59 MN MN A 502 1555 1555 1.97
LINK OD1 ASP A 59 MN MN A 503 1555 1555 2.26
LINK O LEU A 60 MN MN A 502 1555 1555 2.11
LINK OD2 ASP A 151 MN MN A 502 1555 1555 2.09
LINK OD1 ASP A 151 MN MN A 503 1555 1555 2.52
LINK OE2 GLU A 152 MN MN A 503 1555 1555 2.23
LINK O LYS A 262 MN MN A 504 1555 1555 2.47
LINK O ILE A 267 MN MN A 504 1555 1555 2.55
LINK O1G 0KX A 501 MN MN A 502 1555 1555 2.07
LINK O2B 0KX A 501 MN MN A 502 1555 1555 1.96
LINK O2A 0KX A 501 MN MN A 502 1555 1555 2.17
LINK O2A 0KX A 501 MN MN A 503 1555 1555 2.22
CISPEP 1 LYS A 239 PRO A 240 0 -4.37
SITE 1 AC1 22 ASP A 59 LEU A 60 ASP A 61 CYS A 62
SITE 2 AC1 22 PHE A 63 TYR A 64 VAL A 89 THR A 90
SITE 3 AC1 22 TYR A 93 ARG A 96 LYS A 102 ASP A 151
SITE 4 AC1 22 LYS A 239 MN A 502 MN A 503 HOH A 614
SITE 5 AC1 22 HOH A 620 HOH A 638 HOH A 644 DC P 873
SITE 6 AC1 22 DG T 840 DG T 841
SITE 1 AC2 5 ASP A 59 LEU A 60 ASP A 151 0KX A 501
SITE 2 AC2 5 MN A 503
SITE 1 AC3 6 ASP A 59 ASP A 151 GLU A 152 0KX A 501
SITE 2 AC3 6 MN A 502 DC P 873
SITE 1 AC4 4 LYS A 262 ILE A 264 ILE A 267 DC P 872
CRYST1 97.829 97.829 202.887 90.00 90.00 120.00 P 65 2 2 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 0.010222 0.005902 0.000000 0.00000
SCALE2 0.000000 0.011803 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004929 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
