HEADER TRANSFERASE/DNA 21-AUG-18 6M7V
TITLE HUMAN DNA POLYMERASE ETA EXTENSION COMPLEX WITH CDA AT THE -1 POSITION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE ETA;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: RAD30 HOMOLOG A,XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN;
COMPND 5 EC: 2.7.7.7;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: DNA (5'-D(P*GP*TP*GP*TP*GP*AP*GP*T)-3');
COMPND 9 CHAIN: P;
COMPND 10 ENGINEERED: YES;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: DNA (5'-D(P*(02I)P*CP*TP*CP*AP*CP*AP*CP*T)-3');
COMPND 13 CHAIN: T;
COMPND 14 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: HOMO SAPIENS;
SOURCE 11 ORGANISM_COMMON: HUMAN;
SOURCE 12 ORGANISM_TAXID: 9606;
SOURCE 13 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES;
SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 16 ORGANISM_COMMON: HUMAN;
SOURCE 17 ORGANISM_TAXID: 9606
KEYWDS TRANSLESION SYNTHESIS, HUMAN DNA POLYMERSE ETA CDA, TRANSFERASE-DNA
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR P.WENG,Y.GAO,W.YANG
REVDAT 5 11-OCT-23 6M7V 1 LINK
REVDAT 4 25-DEC-19 6M7V 1 REMARK
REVDAT 3 24-OCT-18 6M7V 1 JRNL
REVDAT 2 17-OCT-18 6M7V 1 JRNL
REVDAT 1 12-SEP-18 6M7V 0
JRNL AUTH P.J.WENG,Y.GAO,M.T.GREGORY,P.WANG,Y.WANG,W.YANG
JRNL TITL BYPASSING A 8,5'-CYCLO-2'-DEOXYADENOSINE LESION BY HUMAN DNA
JRNL TITL 2 POLYMERASE ETA AT ATOMIC RESOLUTION.
JRNL REF PROC. NATL. ACAD. SCI. V. 115 10660 2018
JRNL REF 2 U.S.A.
JRNL REFN ESSN 1091-6490
JRNL PMID 30275308
JRNL DOI 10.1073/PNAS.1812856115
REMARK 2
REMARK 2 RESOLUTION. 3.06 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.12_2829: ???)
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) : 3.06
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.18
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 67.6
REMARK 3 NUMBER OF REFLECTIONS : 9898
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.238
REMARK 3 R VALUE (WORKING SET) : 0.237
REMARK 3 FREE R VALUE : 0.268
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700
REMARK 3 FREE R VALUE TEST SET COUNT : 465
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 39.1831 - 8.2869 0.97 757 39 0.2033 0.1974
REMARK 3 2 8.2869 - 6.5877 1.00 732 26 0.2156 0.2207
REMARK 3 3 6.5877 - 5.7580 1.00 708 36 0.2473 0.2688
REMARK 3 4 5.7580 - 5.2328 1.00 702 45 0.2685 0.2349
REMARK 3 5 5.2328 - 4.8585 1.00 700 28 0.2297 0.2632
REMARK 3 6 4.8585 - 4.5725 0.99 691 41 0.2194 0.3266
REMARK 3 7 4.5725 - 4.3438 0.94 662 36 0.2311 0.2919
REMARK 3 8 4.3438 - 4.1550 0.89 619 24 0.2316 0.2675
REMARK 3 9 4.1550 - 3.9952 0.84 578 25 0.2231 0.2958
REMARK 3 10 3.9952 - 3.8574 0.75 509 30 0.2344 0.3280
REMARK 3 11 3.8574 - 3.7369 0.72 504 25 0.2467 0.2856
REMARK 3 12 3.7369 - 3.6302 0.63 436 17 0.2560 0.3289
REMARK 3 13 3.6302 - 3.5347 0.58 398 16 0.2662 0.2399
REMARK 3 14 3.5347 - 3.4485 0.52 365 16 0.2612 0.3375
REMARK 3 15 3.4485 - 3.3701 0.45 305 17 0.2915 0.2959
REMARK 3 16 3.3701 - 3.2984 0.38 255 16 0.2804 0.2869
REMARK 3 17 3.2984 - 3.2325 0.31 214 7 0.3069 0.2893
REMARK 3 18 3.2325 - 3.1715 0.22 146 10 0.3067 0.4554
REMARK 3 19 3.1715 - 3.1149 0.15 96 9 0.3613 0.2888
REMARK 3 20 3.1149 - 3.0621 0.08 56 2 0.4109 0.8534
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) : 0.410
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.860
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
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 : 0.008 3803
REMARK 3 ANGLE : 1.326 5216
REMARK 3 CHIRALITY : 0.073 585
REMARK 3 PLANARITY : 0.014 607
REMARK 3 DIHEDRAL : 25.285 1451
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 6M7V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-18.
REMARK 100 THE DEPOSITION ID IS D_1000236325.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-OCT-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 22-BM
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
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 : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10305
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.050
REMARK 200 RESOLUTION RANGE LOW (A) : 40.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 5.900
REMARK 200 R MERGE (I) : 0.05900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.05
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.16
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 1.04200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400
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: 3SI8
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 65.30
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 16 % PEG 2000 MME 100 MM MES, PH 6.0,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-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 31.53750
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.50300
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.69350
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.50300
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.53750
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.69350
REMARK 290 SMTRY3 4 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: TRIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3200 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 23690 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T
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 GLY A -2
REMARK 465 PRO A -1
REMARK 465 PRO A 154
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 465 THR A 160
REMARK 465 VAL A 161
REMARK 465 GLN A 162
REMARK 465 ALA A 431
REMARK 465 SER A 432
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 8 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DT T 12 O4' - C1' - N1 ANGL. DEV. = 2.5 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 62.02 26.02
REMARK 500 GLN A 38 -66.41 -91.88
REMARK 500 LYS A 43 32.26 -151.41
REMARK 500 ARG A 253 0.29 -69.31
REMARK 500 SER A 257 -1.89 81.69
REMARK 500 ASN A 407 106.69 -41.60
REMARK 500 GLN A 412 -4.88 84.32
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ARG A 234 0.28 SIDE CHAIN
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 503 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD1
REMARK 620 2 MET A 14 O 74.4
REMARK 620 3 ASP A 115 OD1 91.3 91.2
REMARK 620 4 DZ4 A 502 O1A 102.2 175.2 85.4
REMARK 620 5 DZ4 A 502 O1B 171.3 101.2 96.4 82.5
REMARK 620 6 DZ4 A 502 O1G 72.7 69.8 157.6 112.8 98.8
REMARK 620 N 1 2 3 4 5
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 ASP A 13 OD2
REMARK 620 2 ASP A 115 OD2 94.9
REMARK 620 3 GLU A 116 OE2 80.0 93.7
REMARK 620 4 DZ4 A 502 O1A 103.0 100.6 165.0
REMARK 620 5 HOH A 606 O 83.0 177.9 86.1 79.8
REMARK 620 6 DT P 9 OP1 157.5 98.2 80.9 92.6 83.9
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI A 501 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 181 OD2
REMARK 620 2 HIS A 289 NE2 26.8
REMARK 620 3 HIS A 393 NE2 30.7 50.1
REMARK 620 4 HIS A 397 NE2 28.5 48.1 2.2
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 NI A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DZ4 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
DBREF 6M7V A 1 432 UNP Q9Y253 POLH_HUMAN 1 432
DBREF 6M7V P 2 9 PDB 6M7V 6M7V 2 9
DBREF 6M7V T 4 12 PDB 6M7V 6M7V 4 12
SEQADV 6M7V GLY A -2 UNP Q9Y253 EXPRESSION TAG
SEQADV 6M7V PRO A -1 UNP Q9Y253 EXPRESSION TAG
SEQADV 6M7V 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 P 8 DG DT DG DT DG DA DG DT
SEQRES 1 T 9 02I DC DT DC DA DC DA DC DT
HET 02I T 4 21
HET NI A 501 1
HET DZ4 A 502 30
HET MN A 503 1
HET MN A 504 1
HETNAM 02I (6S,7S,8S,10R)-4-AMINO-8-HYDROXY-7,8,9,10-TETRAHYDRO-
HETNAM 2 02I 6H-7,10-EPOXYAZEPINO[1,2-E]PURIN-6-YL DIHYDROGEN
HETNAM 3 02I PHOSPHATE
HETNAM NI NICKEL (II) ION
HETNAM DZ4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 DZ4 PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE
HETNAM MN MANGANESE (II) ION
FORMUL 3 02I C10 H12 N5 O6 P
FORMUL 4 NI NI 2+
FORMUL 5 DZ4 C10 H17 N6 O11 P3
FORMUL 6 MN 2(MN 2+)
FORMUL 8 HOH *17(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 LYS A 69 1 6
HELIX 5 AA5 LEU A 89 SER A 104 1 16
HELIX 6 AA6 LEU A 121 GLN A 133 1 13
HELIX 7 AA7 SER A 138 LEU A 142 5 5
HELIX 8 AA8 GLU A 164 LEU A 178 1 15
HELIX 9 AA9 SER A 185 GLY A 209 1 25
HELIX 10 AB1 ASN A 219 GLY A 228 1 10
HELIX 11 AB2 SER A 239 GLY A 241 5 3
HELIX 12 AB3 SER A 242 GLN A 249 1 8
HELIX 13 AB4 PRO A 251 ILE A 255 5 5
HELIX 14 AB5 GLY A 260 GLY A 271 1 12
HELIX 15 AB6 TYR A 274 PHE A 281 5 8
HELIX 16 AB7 THR A 282 GLY A 291 1 10
HELIX 17 AB8 GLY A 291 CYS A 302 1 12
HELIX 18 AB9 PRO A 326 ALA A 330 5 5
HELIX 19 AC1 ARG A 334 ASP A 360 1 27
HELIX 20 AC2 ASP A 391 ASN A 405 1 15
SHEET 1 AA1 6 ILE A 109 SER A 113 0
SHEET 2 AA1 6 GLU A 116 ASP A 120 -1 O TYR A 118 N GLU A 110
SHEET 3 AA1 6 VAL A 9 MET A 14 -1 N ALA A 10 O VAL A 119
SHEET 4 AA1 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9
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 ILE A 47 VAL A 50 0
SHEET 2 AA2 3 CYS A 34 VAL A 37 -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 PHE A 429 -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 PHE A 429 -1 O ALA A 426 N ILE A 319
SHEET 3 AA5 4 ALA A 363 VAL A 372 -1 N ARG A 371 O THR A 420
SHEET 4 AA5 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368
LINK O3' 02I T 4 P DC T 5 1555 1555 1.60
LINK OD1 ASP A 13 MN MN A 503 1555 1555 2.24
LINK OD2 ASP A 13 MN MN A 504 1555 1555 1.88
LINK O MET A 14 MN MN A 503 1555 1555 2.18
LINK OD1 ASP A 115 MN MN A 503 1555 1555 1.98
LINK OD2 ASP A 115 MN MN A 504 1555 1555 2.08
LINK OE2 GLU A 116 MN MN A 504 1555 1555 2.34
LINK OD2 ASP A 181 NI NI A 501 1555 2554 2.11
LINK NE2 HIS A 289 NI NI A 501 1555 3555 1.78
LINK NE2 HIS A 393 NI NI A 501 1555 1555 2.01
LINK NE2 HIS A 397 NI NI A 501 1555 1555 2.01
LINK O1A DZ4 A 502 MN MN A 503 1555 1555 2.07
LINK O1B DZ4 A 502 MN MN A 503 1555 1555 2.00
LINK O1G DZ4 A 502 MN MN A 503 1555 1555 2.58
LINK O1A DZ4 A 502 MN MN A 504 1555 1555 2.19
LINK MN MN A 504 O HOH A 606 1555 1555 2.44
LINK MN MN A 504 OP1 DT P 9 1555 1555 2.03
CISPEP 1 LEU A 150 PRO A 151 0 -2.04
CISPEP 2 SER A 416 PRO A 417 0 -2.33
SITE 1 AC1 4 ASP A 181 HIS A 289 HIS A 393 HIS A 397
SITE 1 AC2 15 ASP A 13 MET A 14 ASP A 15 CYS A 16
SITE 2 AC2 15 PHE A 17 PHE A 18 ILE A 48 ALA A 49
SITE 3 AC2 15 TYR A 52 ARG A 55 ASP A 115 MN A 503
SITE 4 AC2 15 MN A 504 HOH A 606 DT P 9
SITE 1 AC3 5 ASP A 13 MET A 14 ASP A 115 DZ4 A 502
SITE 2 AC3 5 MN A 504
SITE 1 AC4 7 ASP A 13 ASP A 115 GLU A 116 DZ4 A 502
SITE 2 AC4 7 MN A 503 HOH A 606 DT P 9
CRYST1 63.075 81.387 145.006 90.00 90.00 90.00 P 21 21 21 4
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 0.015854 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012287 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006896 0.00000