PDB Short entry for 3SI8 HEADER TRANSFERASE/DNA 17-JUN-11 3SI8 TITLE HUMAN DNA POLYMERASE ETA - DNA TERNARY COMPLEX WITH THE 5'T OF A CPD TITLE 2 IN THE ACTIVE SITE (TT2) 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(*TP*A*AP*CP*(TTD)P*AP*TP*GP*AP*CP*GP*C)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: DNA TEMPLATE (CHAIN T); COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*TP*GP*CP*GP*TP*CP*AP*TP*A)-3'); COMPND 15 CHAIN: P; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: DNA PRIMER (CHAIN P) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: CHEMICALLY SYNTHESIZED; SOURCE 6 GENE: POLH, RAD30, RAD30A, XPV; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: DNA OLIGONUCLEOTIDE WITH THYMINE DIMER (CYCLOBUTANE SOURCE 14 PYRIMIDINE DIMER, CPD); SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 OTHER_DETAILS: DNA OLIGONUCLEOTIDE KEYWDS PROTEIN-DNA COMPLEX, MULTIPLE DOMAINS, THREE ARE ALPHA/BETA FOLD AND KEYWDS 2 ONE OF THE FOUR IS HELICAL FOLD, DNA POLYMERASE, DNA BINDING, MG2+ KEYWDS 3 AND DNTP BINDING, AFFINITY TAG IS ADDED AND PARTIALLY REMOVED AT THE KEYWDS 4 N-TERMINAL END, NUCLEUS, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.BIERTUMPFEL,Y.ZHAO,Y.KONDO,S.RAMON-MAIQUES,M.GREGORY,J.Y.LEE, AUTHOR 2 C.MASUTANI,A.R.LEHMANN,F.HANAOKA,W.YANG REVDAT 3 13-MAR-24 3SI8 1 COMPND SOURCE REVDAT 2 13-SEP-23 3SI8 1 REMARK SEQADV HETSYN LINK REVDAT 1 03-AUG-11 3SI8 0 SPRSDE 03-AUG-11 3SI8 3MR4 JRNL AUTH C.BIERTUMPFEL,Y.ZHAO,Y.KONDO,S.RAMON-MAIQUES,M.GREGORY, JRNL AUTH 2 J.Y.LEE,C.MASUTANI,A.R.LEHMANN,F.HANAOKA,W.YANG JRNL TITL STRUCTURE AND MECHANISM OF HUMAN DNA POLYMERASE ETA. JRNL REF NATURE V. 465 1044 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20577208 JRNL DOI 10.1038/NATURE09196 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2022865.430 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 37705 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 SET) : 0.241 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2896 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5550 REMARK 3 BIN R VALUE (WORKING SET) : 0.4420 REMARK 3 BIN FREE R VALUE : 0.4410 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 502 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3309 REMARK 3 NUCLEIC ACID ATOMS : 402 REMARK 3 HETEROGEN ATOMS : 135 REMARK 3 SOLVENT ATOMS : 126 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) : 24.59000 REMARK 3 B22 (A**2) : -4.76000 REMARK 3 B33 (A**2) : -19.82000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.61 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.020 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 80.53 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_CB10.PARAM REMARK 3 PARAMETER FILE 3 : LIGANDS0220D.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_CB10.TOP REMARK 3 TOPOLOGY FILE 3 : LIGANDS0220D.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3SI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1000066234. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 : SI 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37705 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : 0.08600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.4300 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) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.59300 REMARK 200 R SYM FOR SHELL (I) : 0.59300 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3MR2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 5 MM MGCL2, 19-21% (W/V) REMARK 280 PEG 2K-MME, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 30.61800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.87950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.12950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.87950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.61800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.12950 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: 7890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 GLY A -2 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 THR A 408 REMARK 465 SER A 409 REMARK 465 GLY A 410 REMARK 465 ALA A 431 REMARK 465 SER A 432 REMARK 465 DT T 1 REMARK 465 DA T 2 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 VAL A 161 CG1 CG2 REMARK 470 GLN A 162 CG CD OE1 NE2 REMARK 470 LYS A 376 CG CD CE NZ REMARK 470 DA T 3 P OP1 OP2 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 61.76 25.59 REMARK 500 LEU A 75 123.96 -38.55 REMARK 500 SER A 217 -156.94 -158.37 REMARK 500 ARG A 253 0.32 -68.85 REMARK 500 SER A 257 -2.50 80.98 REMARK 500 GLN A 314 -32.75 -137.23 REMARK 500 GLN A 412 -6.17 84.58 REMARK 500 THR A 413 -20.68 -140.30 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 450 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 MET A 14 O 73.3 REMARK 620 3 ASP A 115 OD1 91.8 84.2 REMARK 620 4 DZ4 A 433 O1G 91.1 101.7 174.0 REMARK 620 5 DZ4 A 433 O1A 112.5 169.6 86.9 87.1 REMARK 620 6 DZ4 A 433 O1B 164.5 96.5 98.9 79.3 79.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 451 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 ASP A 115 OD2 87.2 REMARK 620 3 GLU A 116 OE2 87.3 93.8 REMARK 620 4 DZ4 A 433 O1A 95.5 98.5 167.5 REMARK 620 5 HOH A 495 O 83.3 170.1 88.6 79.7 REMARK 620 6 DA P 9 O3' 175.8 95.4 89.2 87.4 94.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 452 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 393 NE2 REMARK 620 2 HIS A 397 NE2 105.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DZ4 A 433 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 434 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 435 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 436 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 437 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3D1 A 438 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 439 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 440 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 441 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 442 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTT A 443 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTT A 444 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 445 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 446 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 447 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 448 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 449 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 450 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 452 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MR2 RELATED DB: PDB REMARK 900 RELATED ID: 3MR3 RELATED DB: PDB REMARK 900 RELATED ID: 3MR5 RELATED DB: PDB REMARK 900 RELATED ID: 3MR6 RELATED DB: PDB DBREF 3SI8 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 3SI8 T 1 12 PDB 3SI8 3SI8 1 12 DBREF 3SI8 P 1 9 PDB 3SI8 3SI8 1 9 SEQADV 3SI8 GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 3SI8 PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 3SI8 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 DT DA DA DC TTD DA DT DG DA DC DG DC SEQRES 1 P 9 DT DG DC DG DT DC DA DT DA MODRES 3SI8 TTD T 5 DT CIS-SYN CYCLOBUTANE THYMINE DIMER HET TTD T 5 40 HET DZ4 A 433 30 HET GOL A 434 6 HET GOL A 435 6 HET GOL A 436 6 HET GOL A 437 6 HET 3D1 A 438 18 HET GOL A 439 6 HET GOL A 440 6 HET GOL A 441 6 HET GOL A 442 6 HET DTT A 443 8 HET DTT A 444 8 HET EDO A 445 4 HET EDO A 446 4 HET EDO A 447 4 HET EDO A 448 4 HET EDO A 449 4 HET MG A 450 1 HET MG A 451 1 HET CO A 452 1 HETNAM TTD CIS-SYN CYCLOBUTANE THYMINE DIMER HETNAM DZ4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 DZ4 PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE HETNAM GOL GLYCEROL HETNAM 3D1 (2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2- HETNAM 2 3D1 (HYDROXYMETHYL)FURAN-3-OL HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM CO COBALT (II) ION HETSYN TTD [(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-DIHYDROXY-15A, HETSYN 2 TTD 15B-DIMETHYL-7-OXIDO-13,15,16,18- HETSYN 3 TTD TETRAOXOHEXADECAHYDRO-1H-1,4-EPOX Y-9,12-METHANO-6,8, HETSYN 4 TTD 11-TRIOXA-12A,14,17,18A-TETRAAZA-7- HETSYN 5 TTD PHOSPHACYCLOHEXADECA[1,2,3,4-DEF]BIPHENYLEN-10- HETSYN 6 TTD YL]METHYL DIHYDROGEN PHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 3D1 2'-DEOXYADENOSINE HETSYN DTT 1,4-DITHIOTHREITOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 TTD C20 H28 N4 O15 P2 FORMUL 4 DZ4 C10 H17 N6 O11 P3 FORMUL 5 GOL 8(C3 H8 O3) FORMUL 9 3D1 C10 H13 N5 O3 FORMUL 14 DTT 2(C4 H10 O2 S2) FORMUL 16 EDO 5(C2 H6 O2) FORMUL 21 MG 2(MG 2+) FORMUL 23 CO CO 2+ FORMUL 24 HOH *126(H2 O) HELIX 1 1 CYS A 16 ASN A 26 1 11 HELIX 2 2 PRO A 27 ARG A 30 5 4 HELIX 3 3 SER A 51 ALA A 56 1 6 HELIX 4 4 TRP A 64 CYS A 72 1 9 HELIX 5 5 LEU A 89 ALA A 107 1 19 HELIX 6 6 LEU A 121 GLN A 133 1 13 HELIX 7 7 SER A 138 LEU A 142 5 5 HELIX 8 8 GLN A 162 SER A 177 1 16 HELIX 9 9 SER A 185 GLY A 209 1 25 HELIX 10 10 ASN A 219 GLY A 228 1 10 HELIX 11 11 SER A 239 GLY A 241 5 3 HELIX 12 12 SER A 242 GLN A 249 1 8 HELIX 13 13 PRO A 251 ILE A 255 5 5 HELIX 14 14 GLY A 260 GLY A 271 1 12 HELIX 15 15 TYR A 274 PHE A 281 5 8 HELIX 16 16 THR A 282 GLY A 291 1 10 HELIX 17 17 GLY A 291 CYS A 302 1 12 HELIX 18 18 PRO A 326 ALA A 330 5 5 HELIX 19 19 THR A 333 ASP A 360 1 28 HELIX 20 20 ASP A 391 ASN A 407 1 17 SHEET 1 A 6 ILE A 109 SER A 113 0 SHEET 2 A 6 GLU A 116 ASP A 120 -1 O TYR A 118 N GLU A 110 SHEET 3 A 6 VAL A 9 MET A 14 -1 N ALA A 10 O VAL A 119 SHEET 4 A 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9 SHEET 5 A 6 GLN A 235 LEU A 237 1 O THR A 236 N ILE A 216 SHEET 6 A 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237 SHEET 1 B 3 ILE A 47 VAL A 50 0 SHEET 2 B 3 CYS A 34 VAL A 37 -1 N VAL A 36 O ILE A 48 SHEET 3 B 3 LEU A 76 GLN A 79 1 O ALA A 78 N VAL A 37 SHEET 1 C 2 GLU A 82 SER A 83 0 SHEET 2 C 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83 SHEET 1 D 4 ILE A 319 ASN A 324 0 SHEET 2 D 4 LEU A 419 SER A 430 -1 O ALA A 426 N ILE A 319 SHEET 3 D 4 VAL A 362 VAL A 372 -1 N VAL A 367 O CYS A 425 SHEET 4 D 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368 LINK O3' DC T 4 P TTD T 5 1555 1555 1.61 LINK O3' TTD T 5 P DA T 6 1555 1555 1.61 LINK OD1 ASP A 13 MG MG A 450 1555 1555 2.06 LINK OD2 ASP A 13 MG MG A 451 1555 1555 2.11 LINK O MET A 14 MG MG A 450 1555 1555 2.23 LINK OD1 ASP A 115 MG MG A 450 1555 1555 2.21 LINK OD2 ASP A 115 MG MG A 451 1555 1555 2.28 LINK OE2 GLU A 116 MG MG A 451 1555 1555 1.95 LINK NE2 HIS A 393 CO CO A 452 1555 1555 1.92 LINK NE2 HIS A 397 CO CO A 452 1555 1555 1.86 LINK O1G DZ4 A 433 MG MG A 450 1555 1555 2.27 LINK O1A DZ4 A 433 MG MG A 450 1555 1555 2.35 LINK O1B DZ4 A 433 MG MG A 450 1555 1555 2.39 LINK O1A DZ4 A 433 MG MG A 451 1555 1555 2.43 LINK MG MG A 451 O HOH A 495 1555 1555 2.17 LINK MG MG A 451 O3' DA P 9 1555 1555 2.24 CISPEP 1 LEU A 150 PRO A 151 0 -0.01 CISPEP 2 LYS A 231 PRO A 232 0 0.48 CISPEP 3 SER A 416 PRO A 417 0 -0.47 SITE 1 AC1 18 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC1 18 PHE A 17 PHE A 18 ALA A 49 TYR A 52 SITE 3 AC1 18 ARG A 55 ARG A 61 ASP A 115 LYS A 231 SITE 4 AC1 18 MG A 450 MG A 451 HOH A 475 HOH A 495 SITE 5 AC1 18 DA P 9 TTD T 5 SITE 1 AC2 4 HIS A 240 GLY A 241 PRO A 244 EDO A 449 SITE 1 AC3 3 THR A 282 SER A 284 HOH A 460 SITE 1 AC4 2 THR A 353 ASN A 357 SITE 1 AC5 8 LEU A 11 GLU A 116 LYS A 224 CYS A 227 SITE 2 AC5 8 GLY A 228 LYS A 231 HOH A 495 DA P 9 SITE 1 AC6 5 SER A 257 LEU A 262 LYS A 293 ASN A 294 SITE 2 AC6 5 TRP A 297 SITE 1 AC7 5 ASP A 181 ASN A 182 LEU A 183 GLN A 280 SITE 2 AC7 5 GLN A 285 SITE 1 AC8 3 VAL A 372 ASP A 375 ARG A 377 SITE 1 AC9 2 ASP A 140 LYS A 168 SITE 1 BC1 6 SER A 265 HIS A 289 PHE A 290 GLN A 343 SITE 2 BC1 6 GLN A 346 EDO A 447 SITE 1 BC2 5 GLN A 287 GLY A 291 GLU A 292 GLU A 335 SITE 2 BC2 5 TRP A 339 SITE 1 BC3 6 GLU A 148 GLY A 149 TRP A 174 SER A 239 SITE 2 BC3 6 SER A 242 EDO A 445 SITE 1 BC4 3 GLN A 152 SER A 177 DTT A 444 SITE 1 BC5 5 LYS A 224 ARG A 253 ARG A 256 DT P 8 SITE 2 BC5 5 DA P 9 SITE 1 BC6 1 GOL A 442 SITE 1 BC7 2 ARG A 253 GLY A 260 SITE 1 BC8 3 HIS A 240 ARG A 303 GOL A 434 SITE 1 BC9 5 ASP A 13 MET A 14 ASP A 115 DZ4 A 433 SITE 2 BC9 5 MG A 451 SITE 1 CC1 7 ASP A 13 ASP A 115 GLU A 116 DZ4 A 433 SITE 2 CC1 7 MG A 450 HOH A 495 DA P 9 SITE 1 CC2 4 ASP A 181 HIS A 289 HIS A 393 HIS A 397 CRYST1 61.236 80.259 139.759 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 0.016330 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012460 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007155 0.00000