HEADER TRANSFERASE/DNA 27-AUG-15 5DG9
TITLE CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE ETA INSERTING DGMPNPP ACROSS
TITLE 2 A DNA TEMPLATE CONTAINING 1,N6-ETHENODEOXYADENOSINE LESION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE ETA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 1-432;
COMPND 5 SYNONYM: RAD30 HOMOLOG A,XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN;
COMPND 6 EC: 2.7.7.7;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: DNA (5'-D(*CP*AP*TP*(EDA)P*AP*TP*GP*AP*CP*GP*CP*T)-3');
COMPND 10 CHAIN: T;
COMPND 11 ENGINEERED: YES;
COMPND 12 MOL_ID: 3;
COMPND 13 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3');
COMPND 14 CHAIN: P;
COMPND 15 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: POLH, RAD30, RAD30A, XPV;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 11 ORGANISM_TAXID: 32630;
SOURCE 12 OTHER_DETAILS: CHEMICALLY SYNTHESIZED;
SOURCE 13 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES;
SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 16 ORGANISM_TAXID: 32630;
SOURCE 17 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA POLYMERASE, DNA ENZYME, DNA DAMAGE, TRANSLESION DNA SYNTHESIS,
KEYWDS 2 ETHENO DNA ADDUCTS, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.PATRA,M.EGLI
REVDAT 5 27-SEP-23 5DG9 1 LINK
REVDAT 4 16-JAN-19 5DG9 1 SOURCE JRNL REMARK
REVDAT 3 13-JUL-16 5DG9 1 JRNL
REVDAT 2 15-JUN-16 5DG9 1 JRNL
REVDAT 1 08-JUN-16 5DG9 0
JRNL AUTH A.PATRA,Y.SU,Q.ZHANG,K.M.JOHNSON,F.P.GUENGERICH,M.EGLI
JRNL TITL STRUCTURAL AND KINETIC ANALYSIS OF MISCODING OPPOSITE THE
JRNL TITL 2 DNA ADDUCT 1,N6-ETHENODEOXYADENOSINE BY HUMAN TRANSLESION
JRNL TITL 3 DNA POLYMERASE ETA.
JRNL REF J.BIOL.CHEM. V. 291 14134 2016
JRNL REFN ESSN 1083-351X
JRNL PMID 27226627
JRNL DOI 10.1074/JBC.M116.732487
REMARK 2
REMARK 2 RESOLUTION. 2.15 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1692
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) : 2.15
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.32
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 24768
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.173
REMARK 3 R VALUE (WORKING SET) : 0.170
REMARK 3 FREE R VALUE : 0.222
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970
REMARK 3 FREE R VALUE TEST SET COUNT : 1230
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 42.3234 - 4.4715 1.00 2674 138 0.1770 0.2003
REMARK 3 2 4.4715 - 3.5497 1.00 2625 131 0.1365 0.1580
REMARK 3 3 3.5497 - 3.1012 1.00 2627 143 0.1507 0.2392
REMARK 3 4 3.1012 - 2.8177 1.00 2576 151 0.1724 0.2053
REMARK 3 5 2.8177 - 2.6158 1.00 2576 160 0.1816 0.2818
REMARK 3 6 2.6158 - 2.4616 1.00 2638 127 0.1872 0.2949
REMARK 3 7 2.4616 - 2.3383 1.00 2587 135 0.1902 0.2358
REMARK 3 8 2.3383 - 2.2365 1.00 2640 126 0.2095 0.2811
REMARK 3 9 2.2365 - 2.1504 1.00 2595 119 0.2206 0.2943
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) : 0.260
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.120
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 27.80
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.00
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 3933
REMARK 3 ANGLE : 1.164 5398
REMARK 3 CHIRALITY : 0.043 599
REMARK 3 PLANARITY : 0.005 626
REMARK 3 DIHEDRAL : 19.717 1519
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 5DG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-15.
REMARK 100 THE DEPOSITION ID IS D_1000213141.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-OCT-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : NULL
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 : DIAMOND [111]
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 : 24805
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150
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 (%) : 100.0
REMARK 200 DATA REDUNDANCY : 7.600
REMARK 200 R MERGE (I) : 0.13600
REMARK 200 R SYM (I) : 0.13600
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.40
REMARK 200 R MERGE FOR SHELL (I) : 0.99600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.690
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: 4O3N
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.70
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5.5, 5MM MAGNESIUM
REMARK 280 CHLORIDE, 21% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+5/6
REMARK 290 6555 X-Y,X,Z+1/6
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 27.23733
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 54.47467
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 40.85600
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 68.09333
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 13.61867
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: 5100 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 22010 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P
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 THR A 155
REMARK 465 THR A 156
REMARK 465 ALA A 157
REMARK 465 GLU A 158
REMARK 465 GLU A 159
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 DC T 1 O5' C5' C4' O4' C3' C2' C1'
REMARK 470 DC T 1 N1 C2 O2 N3 C4 N4 C5
REMARK 470 DC T 1 C6
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 737 O HOH A 857 2.07
REMARK 500 O HOH A 829 O HOH A 836 2.11
REMARK 500 OE2 GLU A 116 O HOH A 601 2.11
REMARK 500 O HOH A 717 O HOH A 789 2.12
REMARK 500 O LEU A 315 O HOH A 602 2.15
REMARK 500 OG1 THR A 364 O LYS A 428 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 805 O HOH A 866 5554 2.19
REMARK 500 O HOH A 822 O HOH A 851 2565 2.19
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 DG P 4 O4' - C1' - N9 ANGL. DEV. = 1.8 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 16 66.10 27.37
REMARK 500 TYR A 39 86.22 65.27
REMARK 500 SER A 62 -6.92 72.38
REMARK 500 GLN A 133 43.01 -62.39
REMARK 500 SER A 217 -155.76 -155.26
REMARK 500 SER A 257 -7.95 88.00
REMARK 500 PRO A 312 90.08 -68.76
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 MG A 502 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD1
REMARK 620 2 ASP A 115 OD1 124.4
REMARK 620 3 GLU A 116 OE2 67.4 148.7
REMARK 620 4 XG4 A 501 O1A 96.9 86.1 123.3
REMARK 620 5 HOH A 601 O 67.9 156.1 52.1 71.3
REMARK 620 6 DT P 8 O3' 162.5 73.1 97.5 84.1 96.2
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 503 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD2
REMARK 620 2 MET A 14 O 83.2
REMARK 620 3 ASP A 115 OD2 89.2 83.5
REMARK 620 4 XG4 A 501 O1A 99.6 170.5 87.4
REMARK 620 5 XG4 A 501 O1B 168.2 92.2 101.1 86.8
REMARK 620 6 XG4 A 501 O1G 76.7 101.7 164.1 87.8 93.8
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 XG4 A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5DG7 RELATED DB: PDB
REMARK 900 RELATED ID: 5DG8 RELATED DB: PDB
REMARK 900 RELATED ID: 5DGA RELATED DB: PDB
REMARK 900 RELATED ID: 5DGB RELATED DB: PDB
DBREF 5DG9 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432
DBREF 5DG9 T 1 12 PDB 5DG9 5DG9 1 12
DBREF 5DG9 P 1 8 PDB 5DG9 5DG9 1 8
SEQADV 5DG9 GLY A -2 UNP Q9Y253 EXPRESSION TAG
SEQADV 5DG9 PRO A -1 UNP Q9Y253 EXPRESSION TAG
SEQADV 5DG9 HIS A 0 UNP Q9Y253 EXPRESSION TAG
SEQRES 1 A 435 GLY PRO HIS MET ALA THR GLY GLN ASP ARG VAL VAL ALA
SEQRES 2 A 435 LEU VAL ASP MET ASP CYS PHE PHE VAL GLN VAL GLU GLN
SEQRES 3 A 435 ARG GLN ASN PRO HIS LEU ARG ASN LYS PRO CYS ALA VAL
SEQRES 4 A 435 VAL GLN TYR LYS SER TRP LYS GLY GLY GLY ILE ILE ALA
SEQRES 5 A 435 VAL SER TYR GLU ALA ARG ALA PHE GLY VAL THR ARG SER
SEQRES 6 A 435 MET TRP ALA ASP ASP ALA LYS LYS LEU CYS PRO ASP LEU
SEQRES 7 A 435 LEU LEU ALA GLN VAL ARG GLU SER ARG GLY LYS ALA ASN
SEQRES 8 A 435 LEU THR LYS TYR ARG GLU ALA SER VAL GLU VAL MET GLU
SEQRES 9 A 435 ILE MET SER ARG PHE ALA VAL ILE GLU ARG ALA SER ILE
SEQRES 10 A 435 ASP GLU ALA TYR VAL ASP LEU THR SER ALA VAL GLN GLU
SEQRES 11 A 435 ARG LEU GLN LYS LEU GLN GLY GLN PRO ILE SER ALA ASP
SEQRES 12 A 435 LEU LEU PRO SER THR TYR ILE GLU GLY LEU PRO GLN GLY
SEQRES 13 A 435 PRO THR THR ALA GLU GLU THR VAL GLN LYS GLU GLY MET
SEQRES 14 A 435 ARG LYS GLN GLY LEU PHE GLN TRP LEU ASP SER LEU GLN
SEQRES 15 A 435 ILE ASP ASN LEU THR SER PRO ASP LEU GLN LEU THR VAL
SEQRES 16 A 435 GLY ALA VAL ILE VAL GLU GLU MET ARG ALA ALA ILE GLU
SEQRES 17 A 435 ARG GLU THR GLY PHE GLN CYS SER ALA GLY ILE SER HIS
SEQRES 18 A 435 ASN LYS VAL LEU ALA LYS LEU ALA CYS GLY LEU ASN LYS
SEQRES 19 A 435 PRO ASN ARG GLN THR LEU VAL SER HIS GLY SER VAL PRO
SEQRES 20 A 435 GLN LEU PHE SER GLN MET PRO ILE ARG LYS ILE ARG SER
SEQRES 21 A 435 LEU GLY GLY LYS LEU GLY ALA SER VAL ILE GLU ILE LEU
SEQRES 22 A 435 GLY ILE GLU TYR MET GLY GLU LEU THR GLN PHE THR GLU
SEQRES 23 A 435 SER GLN LEU GLN SER HIS PHE GLY GLU LYS ASN GLY SER
SEQRES 24 A 435 TRP LEU TYR ALA MET CYS ARG GLY ILE GLU HIS ASP PRO
SEQRES 25 A 435 VAL LYS PRO ARG GLN LEU PRO LYS THR ILE GLY CYS SER
SEQRES 26 A 435 LYS ASN PHE PRO GLY LYS THR ALA LEU ALA THR ARG GLU
SEQRES 27 A 435 GLN VAL GLN TRP TRP LEU LEU GLN LEU ALA GLN GLU LEU
SEQRES 28 A 435 GLU GLU ARG LEU THR LYS ASP ARG ASN ASP ASN ASP ARG
SEQRES 29 A 435 VAL ALA THR GLN LEU VAL VAL SER ILE ARG VAL GLN GLY
SEQRES 30 A 435 ASP LYS ARG LEU SER SER LEU ARG ARG CYS CYS ALA LEU
SEQRES 31 A 435 THR ARG TYR ASP ALA HIS LYS MET SER HIS ASP ALA PHE
SEQRES 32 A 435 THR VAL ILE LYS ASN CYS ASN THR SER GLY ILE GLN THR
SEQRES 33 A 435 GLU TRP SER PRO PRO LEU THR MET LEU PHE LEU CYS ALA
SEQRES 34 A 435 THR LYS PHE SER ALA SER
SEQRES 1 T 12 DC DA DT EDA DA DT DG DA DC DG DC DT
SEQRES 1 P 8 DA DG DC DG DT DC DA DT
HET EDA T 4 23
HET XG4 A 501 31
HET MG A 502 1
HET MG A 503 1
HET GOL A 504 6
HETNAM EDA 3-[2-DEOXY-RIBOFURANOSYL]-3H-1,3,4,5A,8-PENTAAZA-AS-
HETNAM 2 EDA INDACENE-5'-MONOPHOSPHATE
HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
HETNAM MG MAGNESIUM ION
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 EDA C12 H14 N5 O6 P
FORMUL 4 XG4 C10 H17 N6 O12 P3
FORMUL 5 MG 2(MG 2+)
FORMUL 7 GOL C3 H8 O3
FORMUL 8 HOH *342(H2 O)
HELIX 1 AA1 CYS A 16 ASN A 26 1 11
HELIX 2 AA2 PRO A 27 ARG A 30 5 4
HELIX 3 AA3 SER A 51 ALA A 56 1 6
HELIX 4 AA4 TRP A 64 CYS A 72 1 9
HELIX 5 AA5 LEU A 89 ALA A 107 1 19
HELIX 6 AA6 LEU A 121 LEU A 132 1 12
HELIX 7 AA7 SER A 138 LEU A 142 5 5
HELIX 8 AA8 GLN A 162 LEU A 178 1 17
HELIX 9 AA9 SER A 185 GLY A 209 1 25
HELIX 10 AB1 ASN A 219 ASN A 230 1 12
HELIX 11 AB2 SER A 242 GLN A 249 1 8
HELIX 12 AB3 MET A 250 ILE A 255 5 6
HELIX 13 AB4 GLY A 260 GLY A 271 1 12
HELIX 14 AB5 TYR A 274 PHE A 281 5 8
HELIX 15 AB6 THR A 282 GLY A 291 1 10
HELIX 16 AB7 GLY A 291 CYS A 302 1 12
HELIX 17 AB8 PRO A 326 ALA A 330 5 5
HELIX 18 AB9 ARG A 334 ASN A 359 1 26
HELIX 19 AC1 ASP A 391 LYS A 404 1 14
HELIX 20 AC2 ASN A 405 ASN A 407 5 3
SHEET 1 AA1 6 VAL A 108 SER A 113 0
SHEET 2 AA1 6 GLU A 116 ASP A 120 -1 O GLU A 116 N ALA A 112
SHEET 3 AA1 6 VAL A 9 MET A 14 -1 N VAL A 12 O ALA A 117
SHEET 4 AA1 6 CYS A 212 SER A 217 -1 O SER A 213 N ASP A 13
SHEET 5 AA1 6 GLN A 235 LEU A 237 1 O THR A 236 N ILE A 216
SHEET 6 AA1 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237
SHEET 1 AA2 3 GLY A 46 VAL A 50 0
SHEET 2 AA2 3 CYS A 34 GLN A 38 -1 N VAL A 36 O ILE A 48
SHEET 3 AA2 3 LEU A 76 GLN A 79 1 O ALA A 78 N VAL A 37
SHEET 1 AA3 2 GLU A 82 SER A 83 0
SHEET 2 AA3 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83
SHEET 1 AA4 3 ILE A 319 ASN A 324 0
SHEET 2 AA4 3 GLU A 414 THR A 427 -1 O ALA A 426 N ILE A 319
SHEET 3 AA4 3 LEU A 331 THR A 333 -1 N ALA A 332 O TRP A 415
SHEET 1 AA5 4 ILE A 319 ASN A 324 0
SHEET 2 AA5 4 GLU A 414 THR A 427 -1 O ALA A 426 N ILE A 319
SHEET 3 AA5 4 GLN A 365 VAL A 372 -1 N VAL A 367 O CYS A 425
SHEET 4 AA5 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368
SHEET 1 AA6 2 ARG A 361 VAL A 362 0
SHEET 2 AA6 2 SER A 430 ALA A 431 -1 O SER A 430 N VAL A 362
LINK O3' DT T 3 P EDA T 4 1555 1555 1.58
LINK O3' EDA T 4 P DA T 5 1555 1555 1.55
LINK OD1 ASP A 13 MG MG A 502 1555 1555 2.23
LINK OD2 ASP A 13 MG MG A 503 1555 1555 2.18
LINK O MET A 14 MG MG A 503 1555 1555 2.23
LINK OD1 ASP A 115 MG MG A 502 1555 1555 2.25
LINK OD2 ASP A 115 MG MG A 503 1555 1555 2.11
LINK OE2 GLU A 116 MG MG A 502 1555 1555 2.54
LINK O1A XG4 A 501 MG MG A 502 1555 1555 2.27
LINK O1A XG4 A 501 MG MG A 503 1555 1555 2.36
LINK O1B XG4 A 501 MG MG A 503 1555 1555 2.06
LINK O1G XG4 A 501 MG MG A 503 1555 1555 1.93
LINK MG MG A 502 O HOH A 601 1555 1555 2.23
LINK MG MG A 502 O3' DT P 8 1555 1555 2.48
CISPEP 1 LEU A 150 PRO A 151 0 -1.75
CISPEP 2 LYS A 231 PRO A 232 0 1.24
CISPEP 3 SER A 416 PRO A 417 0 -5.00
SITE 1 AC1 28 ASP A 13 MET A 14 ASP A 15 CYS A 16
SITE 2 AC1 28 PHE A 17 PHE A 18 GLN A 38 ILE A 48
SITE 3 AC1 28 ALA A 49 TYR A 52 ARG A 55 ARG A 61
SITE 4 AC1 28 ILE A 114 ASP A 115 MG A 502 MG A 503
SITE 5 AC1 28 HOH A 601 HOH A 620 HOH A 627 HOH A 638
SITE 6 AC1 28 HOH A 644 HOH A 679 HOH A 691 HOH A 736
SITE 7 AC1 28 HOH A 774 HOH A 782 DT P 8 EDA T 4
SITE 1 AC2 7 ASP A 13 ASP A 115 GLU A 116 XG4 A 501
SITE 2 AC2 7 MG A 503 HOH A 601 DT P 8
SITE 1 AC3 5 ASP A 13 MET A 14 ASP A 115 XG4 A 501
SITE 2 AC3 5 MG A 502
SITE 1 AC4 10 ARG A 24 PRO A 244 PHE A 247 SER A 248
SITE 2 AC4 10 GLY A 276 GLU A 277 HOH A 643 HOH A 665
SITE 3 AC4 10 HOH A 724 HOH A 729
CRYST1 98.929 98.929 81.712 90.00 90.00 120.00 P 61 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 0.010108 0.005836 0.000000 0.00000
SCALE2 0.000000 0.011672 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012238 0.00000