HEADER TRANSFERASE/DNA 28-APR-10 3MR5 TITLE HUMAN DNA POLYMERASE ETA - DNA TERNARY COMPLEX WITH A CPD 1BP UPSTREAM TITLE 2 OF THE ACTIVE SITE (TT3) 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 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*TP*AP*AP*CP*(TTD)P*AP*TP*GP*AP*CP*GP*A)-3'); COMPND 10 CHAIN: T; COMPND 11 FRAGMENT: DNA TEMPLATE; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: DNA (5'-D(*AP*CP*GP*TP*CP*AP*TP*AP*A)-3'); COMPND 15 CHAIN: P; COMPND 16 FRAGMENT: DNA PRIMER; COMPND 17 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 3MR5 1 REMARK REVDAT 3 21-FEB-24 3MR5 1 REMARK SEQADV HETSYN LINK REVDAT 2 21-MAR-12 3MR5 1 JRNL VERSN REVDAT 1 30-JUN-10 3MR5 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2042276.250 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 42013 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) : 0.191 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.700 REMARK 3 FREE R VALUE TEST SET COUNT : 3253 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6408 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 576 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3347 REMARK 3 NUCLEIC ACID ATOMS : 395 REMARK 3 HETEROGEN ATOMS : 111 REMARK 3 SOLVENT ATOMS : 367 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : -0.17000 REMARK 3 B33 (A**2) : 0.34000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.18 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) : 0.22 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) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.150 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) : 1.240 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.920 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.890 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.840 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 60.20 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 : LIGANDS0238.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 : LIGANDS0238.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3MR5 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_1000058896. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 : 42014 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : 15.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.57500 REMARK 200 FOR SHELL : 2.600 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 (%): 41.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 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 27.23433 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 54.46867 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 40.85150 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 68.08583 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 13.61717 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: 7790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 -1 REMARK 465 THR A 156 REMARK 465 ALA A 157 REMARK 465 GLU A 158 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 LEU A 132 CG CD1 CD2 REMARK 470 THR A 155 OG1 CG2 REMARK 470 GLU A 159 CG CD OE1 OE2 REMARK 470 GLU A 335 CG CD OE1 OE2 REMARK 470 LYS A 376 CG CD CE NZ REMARK 470 ILE A 411 CG1 CG2 CD1 REMARK 470 GLN A 412 CG CD OE1 NE2 REMARK 470 DT T 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DT T 1 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT T 1 C7 C6 REMARK 470 DA T 12 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DA T 12 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA T 12 C2 N3 C4 REMARK 470 DA P 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DA P 1 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA P 1 C2 N3 C4 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 61.92 24.21 REMARK 500 TYR A 39 161.68 70.31 REMARK 500 TYR A 39 116.69 69.88 REMARK 500 SER A 62 -2.23 85.86 REMARK 500 LEU A 183 -146.62 -115.18 REMARK 500 SER A 257 -2.40 85.94 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 444 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 82.5 REMARK 620 3 ASP A 115 OD1 95.7 90.1 REMARK 620 4 XG4 A 433 O1B 166.2 92.5 97.2 REMARK 620 5 XG4 A 433 O1A 102.0 174.0 85.6 84.1 REMARK 620 6 XG4 A 433 O1G 84.7 93.1 176.8 82.8 91.3 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 96.9 REMARK 620 3 GLU A 116 OE2 91.2 91.5 REMARK 620 4 XG4 A 433 O1A 101.7 93.5 165.6 REMARK 620 5 HOH A 448 O 87.9 171.9 94.9 79.2 REMARK 620 6 DA P 9 O3' 171.7 85.6 80.8 86.0 90.5 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 GOL A 443 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XG4 A 444 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL T 13 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL T 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL T 15 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: 3MR6 RELATED DB: PDB DBREF 3MR5 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 3MR5 T 1 12 PDB 3MR5 3MR5 1 12 DBREF 3MR5 P 1 9 PDB 3MR5 3MR5 1 9 SEQADV 3MR5 GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 3MR5 PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 3MR5 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 DA SEQRES 1 P 9 DA DC DG DT DC DA DT DA DA MODRES 3MR5 TTD T 5 DT CIS-SYN CYCLOBUTANE THYMINE DIMER HET TTD T 5 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 GOL A 443 6 HET XG4 A 444 12 HET GOL T 13 6 HET GOL T 14 6 HET GOL T 15 6 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 11(C3 H8 O3) FORMUL 19 HOH *367(H2 O) HELIX 1 1 HIS A 0 GLY A 4 5 5 HELIX 2 2 CYS A 16 ASN A 26 1 11 HELIX 3 3 PRO A 27 ARG A 30 5 4 HELIX 4 4 SER A 51 ALA A 56 1 6 HELIX 5 5 TRP A 64 CYS A 72 1 9 HELIX 6 6 LEU A 89 ALA A 107 1 19 HELIX 7 7 LEU A 121 LYS A 131 1 11 HELIX 8 8 SER A 138 LEU A 142 5 5 HELIX 9 9 GLN A 162 LEU A 178 1 17 HELIX 10 10 SER A 185 GLY A 209 1 25 HELIX 11 11 ASN A 219 ASN A 230 1 12 HELIX 12 12 SER A 239 GLY A 241 5 3 HELIX 13 13 SER A 242 GLN A 249 1 8 HELIX 14 14 MET A 250 ILE A 255 5 6 HELIX 15 15 GLY A 260 GLY A 271 1 12 HELIX 16 16 TYR A 274 PHE A 281 5 8 HELIX 17 17 THR A 282 GLY A 291 1 10 HELIX 18 18 GLY A 291 CYS A 302 1 12 HELIX 19 19 PRO A 326 ALA A 330 5 5 HELIX 20 20 ARG A 334 ASP A 360 1 27 HELIX 21 21 ASP A 391 LYS A 404 1 14 HELIX 22 22 ASN A 405 ASN A 407 5 3 SHEET 1 A 6 VAL A 108 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 GLY A 46 VAL A 50 0 SHEET 2 B 3 CYS A 34 GLN A 38 -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 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' 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 434 1555 1555 2.03 LINK OD2 ASP A 13 MG MG A 435 1555 1555 1.97 LINK O MET A 14 MG MG A 434 1555 1555 2.11 LINK OD1 ASP A 115 MG MG A 434 1555 1555 2.07 LINK OD2 ASP A 115 MG MG A 435 1555 1555 2.08 LINK OE2 GLU A 116 MG MG A 435 1555 1555 2.12 LINK O1B XG4 A 433 MG MG A 434 1555 1555 2.19 LINK O1A XG4 A 433 MG MG A 434 1555 1555 2.22 LINK O1G XG4 A 433 MG MG A 434 1555 1555 2.30 LINK O1A XG4 A 433 MG MG A 435 1555 1555 2.28 LINK MG MG A 435 O HOH A 448 1555 1555 2.15 LINK MG MG A 435 O3' DA P 9 1555 1555 2.28 CISPEP 1 LEU A 150 PRO A 151 0 0.47 CISPEP 2 LYS A 231 PRO A 232 0 -0.09 CISPEP 3 SER A 416 PRO A 417 0 -0.60 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 ILE A 48 ALA A 49 SITE 3 AC1 28 TYR A 52 ARG A 55 ARG A 61 ASP A 115 SITE 4 AC1 28 LYS A 231 MG A 434 MG A 435 HOH A 448 SITE 5 AC1 28 HOH A 466 HOH A 469 HOH A 480 HOH A 481 SITE 6 AC1 28 HOH A 544 HOH A 559 HOH A 610 HOH A 628 SITE 7 AC1 28 DA P 9 HOH P 18 DC T 4 TTD T 5 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 448 DA P 9 SITE 1 AC4 9 ARG A 24 GLN A 25 PRO A 244 SER A 248 SITE 2 AC4 9 GLY A 276 GLU A 277 GOL A 442 HOH A 452 SITE 3 AC4 9 HOH A 571 SITE 1 AC5 8 ARG A 55 ALA A 56 ARG A 361 PHE A 429 SITE 2 AC5 8 HOH A 493 HOH A 510 HOH A 517 HOH A 568 SITE 1 AC6 8 ASP A 13 GLU A 116 LYS A 224 CYS A 227 SITE 2 AC6 8 GLY A 228 HOH A 448 HOH A 480 HOH P 239 SITE 1 AC7 8 GLN A 20 GLN A 23 ARG A 24 ARG A 30 SITE 2 AC7 8 GLY A 209 HOH A 618 HOH A 647 HOH A 740 SITE 1 AC8 8 ILE A 147 GLU A 148 GLY A 149 LEU A 150 SITE 2 AC8 8 ARG A 389 HOH A 508 HOH A 532 HOH A 556 SITE 1 AC9 9 GLN A 5 THR A 184 ASP A 187 ARG A 206 SITE 2 AC9 9 GLU A 207 SER A 239 HIS A 240 GLY A 241 SITE 3 AC9 9 HOH A 485 SITE 1 BC1 10 HIS A 240 VAL A 243 PRO A 244 THR A 279 SITE 2 BC1 10 CYS A 302 ARG A 303 GOL A 436 HOH A 475 SITE 3 BC1 10 HOH A 571 HOH A 717 SITE 1 BC2 8 LYS A 224 ARG A 253 LYS A 254 ILE A 255 SITE 2 BC2 8 ARG A 256 GLY A 259 HOH A 464 DA P 8 SITE 1 BC3 6 SER A 257 LEU A 262 LYS A 293 ASN A 294 SITE 2 BC3 6 TRP A 297 HOH A 636 SITE 1 BC4 5 GLU A 82 ARG A 84 GLY A 85 DC T 10 SITE 2 BC4 5 DG T 11 SITE 1 BC5 2 TTD T 5 DA T 6 SITE 1 BC6 8 ALA A 112 HOH A 564 DA P 8 DA P 9 SITE 2 BC6 8 DA T 6 DT T 7 HOH T 17 HOH T 129 CRYST1 99.125 99.125 81.703 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 0.010088 0.005824 0.000000 0.00000 SCALE2 0.000000 0.011649 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012239 0.00000 CONECT 103 3904 CONECT 104 3905 CONECT 108 3904 CONECT 949 3904 CONECT 950 3905 CONECT 959 3905 CONECT 3527 3538 CONECT 3538 3527 3539 3540 3541 CONECT 3539 3538 CONECT 3540 3538 CONECT 3541 3538 3542 CONECT 3542 3541 3543 CONECT 3543 3542 3544 3545 CONECT 3544 3543 3548 CONECT 3545 3543 3546 3547 CONECT 3546 3545 3558 CONECT 3547 3545 3548 CONECT 3548 3544 3547 3549 CONECT 3549 3548 3550 3557 CONECT 3550 3549 3551 3552 CONECT 3551 3550 CONECT 3552 3550 3553 CONECT 3553 3552 3554 3555 CONECT 3554 3553 CONECT 3555 3553 3556 3557 3572 CONECT 3556 3555 CONECT 3557 3549 3555 3574 CONECT 3558 3546 3559 3560 3561 CONECT 3559 3558 CONECT 3560 3558 CONECT 3561 3558 3562 CONECT 3562 3561 3575 CONECT 3563 3565 3575 CONECT 3564 3565 3576 CONECT 3565 3563 3564 3566 CONECT 3566 3565 3567 3574 CONECT 3567 3566 3568 3569 CONECT 3568 3567 CONECT 3569 3567 3570 CONECT 3570 3569 3571 3572 CONECT 3571 3570 CONECT 3572 3555 3570 3573 3574 CONECT 3573 3572 CONECT 3574 3557 3566 3572 CONECT 3575 3562 3563 3576 CONECT 3576 3564 3575 3577 CONECT 3577 3576 3578 CONECT 3578 3577 CONECT 3859 3905 CONECT 3873 3874 3879 CONECT 3874 3873 3875 3876 CONECT 3875 3874 CONECT 3876 3874 3877 CONECT 3877 3876 3878 3883 CONECT 3878 3877 3879 3881 CONECT 3879 3873 3878 3880 CONECT 3880 3879 CONECT 3881 3878 3882 CONECT 3882 3881 3883 CONECT 3883 3877 3882 3887 CONECT 3884 3888 3892 3897 3903 CONECT 3885 3889 3893 3897 3898 CONECT 3886 3890 3894 3898 3899 CONECT 3887 3883 3891 3901 CONECT 3888 3884 3904 3905 CONECT 3889 3885 3904 CONECT 3890 3886 3904 CONECT 3891 3887 3895 CONECT 3892 3884 CONECT 3893 3885 CONECT 3894 3886 CONECT 3895 3891 3896 3900 CONECT 3896 3895 CONECT 3897 3884 3885 CONECT 3898 3885 3886 CONECT 3899 3886 CONECT 3900 3895 3901 3902 CONECT 3901 3887 3900 CONECT 3902 3900 3903 CONECT 3903 3884 3902 CONECT 3904 103 108 949 3888 CONECT 3904 3889 3890 CONECT 3905 104 950 959 3859 CONECT 3905 3888 3987 CONECT 3906 3907 3908 CONECT 3907 3906 CONECT 3908 3906 3909 3910 CONECT 3909 3908 CONECT 3910 3908 3911 CONECT 3911 3910 CONECT 3912 3913 3914 CONECT 3913 3912 CONECT 3914 3912 3915 3916 CONECT 3915 3914 CONECT 3916 3914 3917 CONECT 3917 3916 CONECT 3918 3919 3920 CONECT 3919 3918 CONECT 3920 3918 3921 3922 CONECT 3921 3920 CONECT 3922 3920 3923 CONECT 3923 3922 CONECT 3924 3925 3926 CONECT 3925 3924 CONECT 3926 3924 3927 3928 CONECT 3927 3926 CONECT 3928 3926 3929 CONECT 3929 3928 CONECT 3930 3931 3932 CONECT 3931 3930 CONECT 3932 3930 3933 3934 CONECT 3933 3932 CONECT 3934 3932 3935 CONECT 3935 3934 CONECT 3936 3937 3938 CONECT 3937 3936 CONECT 3938 3936 3939 3940 CONECT 3939 3938 CONECT 3940 3938 3941 CONECT 3941 3940 CONECT 3942 3943 3944 CONECT 3943 3942 CONECT 3944 3942 3945 3946 CONECT 3945 3944 CONECT 3946 3944 3947 CONECT 3947 3946 CONECT 3948 3949 3950 CONECT 3949 3948 CONECT 3950 3948 3951 3952 CONECT 3951 3950 CONECT 3952 3950 3953 CONECT 3953 3952 CONECT 3954 3955 3960 CONECT 3955 3954 3956 3957 CONECT 3956 3955 CONECT 3957 3955 3958 CONECT 3958 3957 3959 3964 CONECT 3959 3958 3960 3962 CONECT 3960 3954 3959 3961 CONECT 3961 3960 CONECT 3962 3959 3963 CONECT 3963 3962 3964 CONECT 3964 3958 3963 3965 CONECT 3965 3964 CONECT 3966 3967 3968 CONECT 3967 3966 CONECT 3968 3966 3969 3970 CONECT 3969 3968 CONECT 3970 3968 3971 CONECT 3971 3970 CONECT 3972 3973 3974 CONECT 3973 3972 CONECT 3974 3972 3975 3976 CONECT 3975 3974 CONECT 3976 3974 3977 CONECT 3977 3976 CONECT 3978 3979 3980 CONECT 3979 3978 CONECT 3980 3978 3981 3982 CONECT 3981 3980 CONECT 3982 3980 3983 CONECT 3983 3982 CONECT 3987 3905 MASTER 389 0 16 22 18 0 37 6 4220 3 163 36 END