HEADER TRANSFERASE/DNA 12-NOV-14 4RT2
TITLE TERNARY COMPLEX CRYSTAL STRUCTURE OF DNA POLYMERASE BETA WITH (ALPHA,
TITLE 2 BETA)-CH2-(BETA,GAMMA)-NH-DTTP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE BETA;
COMPND 3 CHAIN: A;
COMPND 4 EC: 2.7.7.7, 4.2.99.-;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-
COMPND 8 3');
COMPND 9 CHAIN: T;
COMPND 10 SYNONYM: TEMPLATE STRAND;
COMPND 11 ENGINEERED: YES;
COMPND 12 MOL_ID: 3;
COMPND 13 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3');
COMPND 14 CHAIN: P;
COMPND 15 SYNONYM: PRIMER STRAND;
COMPND 16 ENGINEERED: YES;
COMPND 17 MOL_ID: 4;
COMPND 18 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3');
COMPND 19 CHAIN: D;
COMPND 20 SYNONYM: DOWNSTREAM PRIMER STRAND;
COMPND 21 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: POLB;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PWL11;
SOURCE 10 MOL_ID: 2;
SOURCE 11 SYNTHETIC: YES;
SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 13 ORGANISM_TAXID: 32630;
SOURCE 14 MOL_ID: 3;
SOURCE 15 SYNTHETIC: YES;
SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 17 ORGANISM_TAXID: 32630;
SOURCE 18 MOL_ID: 4;
SOURCE 19 SYNTHETIC: YES;
SOURCE 20 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 21 ORGANISM_TAXID: 32630
KEYWDS DNA POLYMERASE BETA, CONFORMATIONAL CHANGE, ENZYME MECHANISM,
KEYWDS 2 TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR V.K.BATRA,S.H.WILSON
REVDAT 3 20-SEP-23 4RT2 1 REMARK LINK
REVDAT 2 22-NOV-17 4RT2 1 REMARK
REVDAT 1 01-JUL-15 4RT2 0
JRNL AUTH A.P.KADINA,B.A.KASHEMIROV,K.OERTELL,V.K.BATRA,S.H.WILSON,
JRNL AUTH 2 M.F.GOODMAN,C.E.MCKENNA
JRNL TITL TWO SCAFFOLDS FROM TWO FLIPS: (ALPHA, BETA)/(BETA, GAMMA)
JRNL TITL 2 CH2/NH "MET-IM" ANALOGUES OF DTTP.
JRNL REF ORG.LETT. V. 17 2586 2015
JRNL REFN ISSN 1523-7060
JRNL PMID 25970636
JRNL DOI 10.1021/ACS.ORGLETT.5B00799
REMARK 2
REMARK 2 RESOLUTION. 1.92 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.24
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0
REMARK 3 NUMBER OF REFLECTIONS : 30033
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.179
REMARK 3 R VALUE (WORKING SET) : 0.176
REMARK 3 FREE R VALUE : 0.211
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.650
REMARK 3 FREE R VALUE TEST SET COUNT : 1997
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 21.2399 - 4.6129 0.99 2160 153 0.1425 0.1508
REMARK 3 2 4.6129 - 3.6675 0.98 2110 150 0.1380 0.1502
REMARK 3 3 3.6675 - 3.2057 0.99 2118 151 0.1558 0.1892
REMARK 3 4 3.2057 - 2.9134 0.98 2078 149 0.2014 0.2626
REMARK 3 5 2.9134 - 2.7050 0.98 2101 150 0.2125 0.2559
REMARK 3 6 2.7050 - 2.5458 0.98 2059 147 0.2064 0.2521
REMARK 3 7 2.5458 - 2.4185 0.97 2051 146 0.2060 0.2530
REMARK 3 8 2.4185 - 2.3134 0.97 2080 149 0.1924 0.2269
REMARK 3 9 2.3134 - 2.2244 0.97 2071 146 0.1923 0.2614
REMARK 3 10 2.2244 - 2.1477 0.97 2046 145 0.1926 0.2376
REMARK 3 11 2.1477 - 2.0806 0.96 2046 146 0.1973 0.2374
REMARK 3 12 2.0806 - 2.0212 0.95 2009 143 0.2175 0.2861
REMARK 3 13 2.0212 - 1.9680 0.82 1732 124 0.2312 0.2646
REMARK 3 14 1.9680 - 1.9200 0.65 1375 98 0.2691 0.3406
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
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) : 0.210
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.310
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.37
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 : 0.007 3392
REMARK 3 ANGLE : 1.020 4703
REMARK 3 CHIRALITY : 0.042 514
REMARK 3 PLANARITY : 0.005 496
REMARK 3 DIHEDRAL : 19.637 1329
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 4RT2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-14.
REMARK 100 THE DEPOSITION ID IS D_1000087760.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-FEB-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
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 HF
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54108
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30067
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : 0.08400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99
REMARK 200 COMPLETENESS FOR SHELL (%) : 67.4
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : 0.49300
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: PHENIX
REMARK 200 STARTING MODEL: PDB ENTRY 2FMS
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.73
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 16-18% PEG3350, PH 7.5, VAPOR
REMARK 280 DIFFUSION, TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 39.70450
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 5540 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19860 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, 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 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 1
REMARK 465 SER A 2
REMARK 465 LYS A 3
REMARK 465 ARG A 4
REMARK 465 LYS A 5
REMARK 465 ALA A 6
REMARK 465 PRO A 7
REMARK 465 GLN A 8
REMARK 465 GLU A 9
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 248 CG CD CE NZ
REMARK 470 VAL A 303 CG1 CG2
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 T 129 O HOH T 151 1.85
REMARK 500 O HOH A 749 O HOH A 789 1.87
REMARK 500 OP1 DC T 16 O HOH T 149 1.90
REMARK 500 OP2 DA T 6 O HOH T 126 1.92
REMARK 500 O HOH P 103 O HOH P 115 1.98
REMARK 500 O HOH T 128 O HOH T 132 2.06
REMARK 500 O HOH A 735 O HOH A 740 2.12
REMARK 500 O HOH T 128 O HOH T 139 2.12
REMARK 500 O HOH T 115 O HOH T 125 2.15
REMARK 500 O HOH A 686 O HOH A 802 2.16
REMARK 500 O HOH P 111 O HOH P 112 2.17
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 DC T 8 O3' DC T 8 C3' -0.037
REMARK 500 DG D 1 P DG D 1 OP3 -0.121
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
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 ATM2 ATM3
REMARK 500 DC T 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
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 178 -136.11 -113.51
REMARK 500 ASN A 294 -168.40 -126.68
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 NA A 404 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS A 60 O
REMARK 620 2 LEU A 62 O 98.4
REMARK 620 3 VAL A 65 O 86.6 97.9
REMARK 620 4 HOH A 533 O 94.1 86.4 175.4
REMARK 620 5 DC D 3 OP1 167.0 94.5 89.8 88.5
REMARK 620 6 HOH D 112 O 88.2 170.7 88.9 86.6 79.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 403 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 THR A 101 O
REMARK 620 2 VAL A 103 O 94.6
REMARK 620 3 ILE A 106 O 94.8 87.5
REMARK 620 4 HOH A 553 O 83.5 84.5 171.7
REMARK 620 5 DG P 9 OP1 162.9 96.9 98.2 85.1
REMARK 620 6 HOH P 101 O 81.2 175.8 93.4 94.3 87.0
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 401 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 190 OD1
REMARK 620 2 ASP A 192 OD2 97.7
REMARK 620 3 N6T A 406 O3G 86.8 175.5
REMARK 620 4 N6T A 406 O2B 172.7 88.9 86.6
REMARK 620 5 N6T A 406 O1A 94.9 89.7 90.7 88.2
REMARK 620 6 HOH A 505 O 85.8 88.2 91.5 91.4 177.8
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 402 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 190 OD2
REMARK 620 2 ASP A 192 OD1 107.7
REMARK 620 3 ASP A 256 OD2 105.4 95.3
REMARK 620 4 N6T A 406 O1A 88.1 92.0 161.8
REMARK 620 5 HOH A 665 O 85.5 163.4 90.6 78.1
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE N6T A 406
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4RT3 RELATED DB: PDB
DBREF 4RT2 A 1 335 UNP P06746 DPOLB_HUMAN 1 335
DBREF 4RT2 T 1 16 PDB 4RT2 4RT2 1 16
DBREF 4RT2 P 1 10 PDB 4RT2 4RT2 1 10
DBREF 4RT2 D 1 5 PDB 4RT2 4RT2 1 5
SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY
SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU
SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR
SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS
SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL
SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA
SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP
SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER
SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU
SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP
SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE
SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU
SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL
SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG
SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU
SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO
SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL
SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS
SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU
SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE
SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR
SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA
SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG
SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO
SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP
SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU
SEQRES 1 T 16 DC DC DG DA DC DA DG DC DG DC DA DT DC
SEQRES 2 T 16 DA DG DC
SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DOC
SEQRES 1 D 5 DG DT DC DG DG
MODRES 4RT2 DOC P 10 DC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
HET DOC P 10 18
HET MG A 401 1
HET NA A 402 1
HET NA A 403 1
HET NA A 404 1
HET CL A 405 1
HET N6T A 406 29
HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
HETNAM MG MAGNESIUM ION
HETNAM NA SODIUM ION
HETNAM CL CHLORIDE ION
HETNAM N6T 2'-DEOXY-5'-O-[(S)-HYDROXY{[(S)-
HETNAM 2 N6T HYDROXY(PHOSPHONOAMINO)PHOSPHORYL]METHYL}PHOSPHORYL]-
HETNAM 3 N6T 3,4-DIHYDROTHYMIDINE
FORMUL 3 DOC C9 H14 N3 O6 P
FORMUL 5 MG MG 2+
FORMUL 6 NA 3(NA 1+)
FORMUL 9 CL CL 1-
FORMUL 10 N6T C11 H20 N3 O12 P3
FORMUL 11 HOH *387(H2 O)
HELIX 1 1 ASN A 12 VAL A 29 1 18
HELIX 2 2 ALA A 32 TYR A 49 1 18
HELIX 3 3 SER A 55 LYS A 61 1 7
HELIX 4 4 GLY A 66 GLY A 80 1 15
HELIX 5 5 LEU A 82 ASP A 91 1 10
HELIX 6 6 ASP A 91 THR A 101 1 11
HELIX 7 7 GLY A 107 GLU A 117 1 11
HELIX 8 8 THR A 121 ASN A 128 1 8
HELIX 9 9 GLU A 129 LEU A 132 5 4
HELIX 10 10 ASN A 133 TYR A 142 1 10
HELIX 11 11 TYR A 142 LYS A 148 1 7
HELIX 12 12 ARG A 152 ASP A 170 1 19
HELIX 13 13 CYS A 178 ARG A 183 1 6
HELIX 14 14 LYS A 209 VAL A 221 1 13
HELIX 15 15 PRO A 261 ASP A 263 5 3
HELIX 16 16 GLN A 264 GLY A 274 1 11
HELIX 17 17 SER A 275 LYS A 289 1 15
HELIX 18 18 SER A 315 ILE A 323 1 9
HELIX 19 19 GLU A 329 ARG A 333 5 5
SHEET 1 A 2 ILE A 150 PRO A 151 0
SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150
SHEET 1 B 5 ILE A 174 VAL A 177 0
SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176
SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195
SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253
SHEET 5 B 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236
SHEET 1 C 2 PHE A 291 ILE A 293 0
SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292
LINK O3' DG P 9 P DOC P 10 1555 1555 1.61
LINK O LYS A 60 NA NA A 404 1555 1555 2.42
LINK O LEU A 62 NA NA A 404 1555 1555 2.31
LINK O VAL A 65 NA NA A 404 1555 1555 2.49
LINK O THR A 101 NA NA A 403 1555 1555 2.35
LINK O VAL A 103 NA NA A 403 1555 1555 2.49
LINK O ILE A 106 NA NA A 403 1555 1555 2.42
LINK OD1 ASP A 190 MG MG A 401 1555 1555 1.93
LINK OD2 ASP A 190 NA NA A 402 1555 1555 2.10
LINK OD2 ASP A 192 MG MG A 401 1555 1555 2.03
LINK OD1 ASP A 192 NA NA A 402 1555 1555 2.10
LINK OD2 ASP A 256 NA NA A 402 1555 1555 2.13
LINK MG MG A 401 O3G N6T A 406 1555 1555 2.05
LINK MG MG A 401 O2B N6T A 406 1555 1555 2.10
LINK MG MG A 401 O1A N6T A 406 1555 1555 2.14
LINK MG MG A 401 O HOH A 505 1555 1555 2.07
LINK NA NA A 402 O1A N6T A 406 1555 1555 2.40
LINK NA NA A 402 O HOH A 665 1555 1555 2.11
LINK NA NA A 403 O HOH A 553 1555 1555 2.76
LINK NA NA A 403 OP1 DG P 9 1555 1555 2.45
LINK NA NA A 403 O HOH P 101 1555 1555 2.46
LINK NA NA A 404 O HOH A 533 1555 1555 2.41
LINK NA NA A 404 OP1 DC D 3 1555 1555 2.71
LINK NA NA A 404 O HOH D 112 1555 1555 2.72
CISPEP 1 GLY A 274 SER A 275 0 0.51
SITE 1 AC1 5 ASP A 190 ASP A 192 NA A 402 N6T A 406
SITE 2 AC1 5 HOH A 505
SITE 1 AC2 6 ASP A 190 ASP A 192 ASP A 256 MG A 401
SITE 2 AC2 6 N6T A 406 HOH A 665
SITE 1 AC3 6 THR A 101 VAL A 103 ILE A 106 HOH A 553
SITE 2 AC3 6 DG P 9 HOH P 101
SITE 1 AC4 6 LYS A 60 LEU A 62 VAL A 65 HOH A 533
SITE 2 AC4 6 DC D 3 HOH D 112
SITE 1 AC5 4 ALA A 32 ILE A 33 HIS A 34 LYS A 35
SITE 1 AC6 27 GLY A 179 SER A 180 ARG A 183 SER A 188
SITE 2 AC6 27 GLY A 189 ASP A 190 ASP A 192 TYR A 271
SITE 3 AC6 27 PHE A 272 THR A 273 GLY A 274 ASP A 276
SITE 4 AC6 27 ASN A 279 MG A 401 NA A 402 HOH A 505
SITE 5 AC6 27 HOH A 511 HOH A 575 HOH A 591 HOH A 592
SITE 6 AC6 27 HOH A 607 HOH A 665 HOH A 711 HOH A 742
SITE 7 AC6 27 HOH A 771 DOC P 10 DA T 6
CRYST1 50.587 79.409 55.315 90.00 107.27 90.00 P 1 21 1 2
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 0.019768 0.000000 0.006147 0.00000
SCALE2 0.000000 0.012593 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018932 0.00000