PDB Short entry for 3MR6 HEADER TRANSFERASE/DNA 28-APR-10 3MR6 TITLE HUMAN DNA POLYMERASE ETA - DNA TERNARY COMPLEX WITH A CPD 2BP UPSTREAM TITLE 2 OF THE ACTIVE SITE (TT4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE ETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC CORE (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 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*C*AP*TP*CP*AP*(TTD)P*AP*CP*GP*AP*GP*C)-3'); COMPND 11 CHAIN: T; COMPND 12 FRAGMENT: DNA TEMPLATE; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'-D(*TP*CP*TP*CP*GP*TP*AP*AP*T)-3'); COMPND 16 CHAIN: P; COMPND 17 FRAGMENT: DNA PRIMER; COMPND 18 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 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS POL ETA, POLYMERASE, THYMINE DIMER, CPD, XPV, XERODERMA PIGMENTOSUM KEYWDS 2 VARIANT, DNA DAMAGE, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.BIERTUMPFEL,Y.ZHAO,S.RAMON-MAIQUES,M.T.GREGORY,J.Y.LEE,W.YANG REVDAT 4 03-APR-24 3MR6 1 REMARK REVDAT 3 21-FEB-24 3MR6 1 REMARK SEQADV HETSYN LINK REVDAT 2 21-MAR-12 3MR6 1 JRNL VERSN REVDAT 1 30-JUN-10 3MR6 0 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. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2174452.590 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 34965 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) : 0.196 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.600 REMARK 3 FREE R VALUE TEST SET COUNT : 2664 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5341 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 434 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3340 REMARK 3 NUCLEIC ACID ATOMS : 390 REMARK 3 HETEROGEN ATOMS : 87 REMARK 3 SOLVENT ATOMS : 357 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.66000 REMARK 3 B22 (A**2) : -1.66000 REMARK 3 B33 (A**2) : 3.32000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.660 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) : 1.280 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.940 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.830 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.630 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 58.13 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : LIGANDS0143.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 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : LIGANDS0143.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3MR6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000058897. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 95 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 : 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 : 34967 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 29.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.53400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.290 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: UNPUBLISHED STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 5 MM MGCL2, 6-21% (W/V) PEG REMARK 280 2K-MME, STREAK/MICRO SEEDING, PH 6.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 27.34867 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 54.69733 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 41.02300 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 68.37167 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 13.67433 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: 6560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 465 THR A 160 REMARK 465 ILE A 411 REMARK 465 GLN A 412 REMARK 465 DC T 1 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 376 CG CD CE NZ REMARK 470 DA T 2 P OP1 OP2 REMARK 470 DC T 12 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC T 12 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC T 12 C6 REMARK 470 DT P 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT P 1 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT P 1 C7 C6 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 ARG A 128 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 PRO A 136 C - N - CD ANGL. DEV. = -13.8 DEGREES REMARK 500 DT T 3 O4' - C4' - C3' ANGL. DEV. = -3.6 DEGREES REMARK 500 DT T 3 C1' - O4' - C4' ANGL. DEV. = -10.0 DEGREES REMARK 500 DT T 3 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 DT T 3 C6 - N1 - C1' ANGL. DEV. = -11.8 DEGREES REMARK 500 DT T 3 C2 - N1 - C1' ANGL. DEV. = 12.3 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 59.10 23.97 REMARK 500 TYR A 39 88.67 77.31 REMARK 500 TYR A 39 166.59 70.50 REMARK 500 LYS A 40 -29.85 -144.17 REMARK 500 LEU A 183 -140.95 -118.17 REMARK 500 SER A 257 -1.12 87.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 XG4 A 443 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 434 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 MET A 14 O 81.4 REMARK 620 3 ASP A 115 OD1 93.4 87.2 REMARK 620 4 XG4 A 433 O1B 166.3 90.7 97.4 REMARK 620 5 XG4 A 433 O1A 103.5 172.8 87.2 85.4 REMARK 620 6 XG4 A 433 O1G 86.8 91.8 179.0 82.2 93.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 435 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 ASP A 115 OD2 91.7 REMARK 620 3 GLU A 116 OE2 88.1 89.7 REMARK 620 4 XG4 A 433 O1A 100.5 91.6 171.3 REMARK 620 5 HOH A 479 O 91.4 171.1 98.7 79.6 REMARK 620 6 DT P 9 O3' 170.3 91.1 82.7 88.7 87.2 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 433 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 434 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG 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 GOL 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 XG4 A 443 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: 3MR4 RELATED DB: PDB REMARK 900 RELATED ID: 3MR5 RELATED DB: PDB DBREF 3MR6 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 3MR6 T 1 12 PDB 3MR6 3MR6 1 12 DBREF 3MR6 P 1 9 PDB 3MR6 3MR6 1 9 SEQADV 3MR6 GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 3MR6 PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 3MR6 HIS A 0 UNP Q9Y253 EXPRESSION TAG SEQADV 3MR6 MET A 406 UNP Q9Y253 CYS 406 ENGINEERED MUTATION 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 MET 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 DC DA TTD DA DC DG DA DG DC SEQRES 1 P 9 DT DC DT DC DG DT DA DA DT MODRES 3MR6 TTD T 6 DT CIS-SYN CYCLOBUTANE THYMINE DIMER HET TTD T 6 40 HET XG4 A 433 31 HET MG A 434 1 HET MG A 435 1 HET GOL A 436 6 HET GOL A 437 6 HET GOL A 438 6 HET GOL A 439 6 HET GOL A 440 6 HET GOL A 441 6 HET GOL A 442 6 HET XG4 A 443 12 HETNAM TTD CIS-SYN CYCLOBUTANE THYMINE DIMER 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 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 FORMUL 2 TTD C20 H28 N4 O15 P2 FORMUL 4 XG4 2(C10 H17 N6 O12 P3) FORMUL 5 MG 2(MG 2+) FORMUL 7 GOL 7(C3 H8 O3) FORMUL 15 HOH *357(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 ALA A 65 CYS A 72 1 8 HELIX 5 5 LEU A 89 ALA A 107 1 19 HELIX 6 6 LEU A 121 LYS A 131 1 11 HELIX 7 7 SER A 138 LEU A 142 5 5 HELIX 8 8 GLN A 162 LEU A 178 1 17 HELIX 9 9 SER A 185 GLY A 209 1 25 HELIX 10 10 ASN A 219 ASN A 230 1 12 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 MET A 250 ILE A 255 5 6 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 CYS A 302 1 21 HELIX 17 17 PRO A 326 ALA A 330 5 5 HELIX 18 18 ARG A 334 ASP A 360 1 27 HELIX 19 19 ASP A 391 LYS A 404 1 14 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 ALA A 214 SHEET 6 A 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237 SHEET 1 B 4 MET A 63 TRP A 64 0 SHEET 2 B 4 GLY A 46 VAL A 50 -1 N ILE A 47 O MET A 63 SHEET 3 B 4 CYS A 34 GLN A 38 -1 N VAL A 36 O ILE A 48 SHEET 4 B 4 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 3 ILE A 319 ASN A 324 0 SHEET 2 D 3 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 D 3 LEU A 331 THR A 333 -1 N ALA A 332 O TRP A 415 SHEET 1 E 4 ILE A 319 ASN A 324 0 SHEET 2 E 4 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 E 4 ARG A 361 VAL A 372 -1 N VAL A 367 O CYS A 425 SHEET 4 E 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368 LINK O3' DA T 5 P TTD T 6 1555 1555 1.61 LINK O3' TTD T 6 P DA T 7 1555 1555 1.61 LINK OD1 ASP A 13 MG MG A 434 1555 1555 2.02 LINK OD2 ASP A 13 MG MG A 435 1555 1555 2.02 LINK O MET A 14 MG MG A 434 1555 1555 2.14 LINK OD1 ASP A 115 MG MG A 434 1555 1555 2.07 LINK OD2 ASP A 115 MG MG A 435 1555 1555 2.16 LINK OE2 GLU A 116 MG MG A 435 1555 1555 2.15 LINK O1B XG4 A 433 MG MG A 434 1555 1555 2.11 LINK O1A XG4 A 433 MG MG A 434 1555 1555 2.17 LINK O1G XG4 A 433 MG MG A 434 1555 1555 2.24 LINK O1A XG4 A 433 MG MG A 435 1555 1555 2.31 LINK MG MG A 435 O HOH A 479 1555 1555 2.27 LINK MG MG A 435 O3' DT P 9 1555 1555 2.15 CISPEP 1 LEU A 150 PRO A 151 0 0.28 CISPEP 2 LYS A 231 PRO A 232 0 5.07 CISPEP 3 SER A 416 PRO A 417 0 -0.68 SITE 1 AC1 27 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC1 27 PHE A 17 PHE A 18 ILE A 48 TYR A 52 SITE 3 AC1 27 ARG A 55 ARG A 61 ASP A 115 LYS A 231 SITE 4 AC1 27 MG A 434 MG A 435 GOL A 438 HOH A 476 SITE 5 AC1 27 HOH A 479 HOH A 483 HOH A 488 HOH A 584 SITE 6 AC1 27 HOH A 596 DT P 9 HOH P 59 HOH P 151 SITE 7 AC1 27 DC T 4 DA T 5 HOH T 61 SITE 1 AC2 5 ASP A 13 MET A 14 ASP A 115 XG4 A 433 SITE 2 AC2 5 MG A 435 SITE 1 AC3 7 ASP A 13 ASP A 115 GLU A 116 XG4 A 433 SITE 2 AC3 7 MG A 434 HOH A 479 DT P 9 SITE 1 AC4 9 VAL A 97 LEU A 315 PRO A 316 ASN A 359 SITE 2 AC4 9 HOH A 484 HOH A 517 HOH A 527 HOH A 582 SITE 3 AC4 9 HOH A 742 SITE 1 AC5 9 ARG A 24 PRO A 244 PHE A 247 SER A 248 SITE 2 AC5 9 GLY A 276 GLU A 277 HOH A 448 HOH A 451 SITE 3 AC5 9 HOH A 623 SITE 1 AC6 6 TYR A 52 ARG A 55 GLY A 228 LYS A 231 SITE 2 AC6 6 XG4 A 433 HOH A 602 SITE 1 AC7 7 ASN A 26 LEU A 77 ALA A 78 GLN A 287 SITE 2 AC7 7 HOH A 513 HOH A 607 HOH A 682 SITE 1 AC8 7 SER A 104 ALA A 107 VAL A 108 ILE A 109 SITE 2 AC8 7 PRO A 312 ARG A 313 GLN A 314 SITE 1 AC9 2 GLN A 280 GLN A 285 SITE 1 BC1 6 GLU A 94 ALA A 95 GLU A 98 ARG A 303 SITE 2 BC1 6 HOH A 445 HOH A 670 SITE 1 BC2 4 SER A 257 LYS A 293 ASN A 294 TRP A 297 CRYST1 98.044 98.044 82.046 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 0.010200 0.005889 0.000000 0.00000 SCALE2 0.000000 0.011777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012188 0.00000