HEADER TRANSFERASE 31-JUL-19 6PZ3 TITLE POLYMERASE ETA-CATALYZED INSERTION OF CORRECT G OPPOSITE TEMPLATE TITLE 2 CYTARABINE (ARAC) RESIDUE 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 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA PRIMER STRAND; COMPND 10 CHAIN: P; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA TEMPLATE CONTAINING CYTARABINE (ARAC) RESIDUE; COMPND 14 CHAIN: T; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLH, RAD30, RAD30A, XPV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS CYTARABIN, LESION BYPASS, DNA DAMAGE, REPLICATION, CHEMOTHERAPY, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR O.RECHKOBLIT,A.K.AGGARWAL REVDAT 3 13-MAR-24 6PZ3 1 LINK REVDAT 2 04-DEC-19 6PZ3 1 REMARK REVDAT 1 20-NOV-19 6PZ3 0 JRNL AUTH O.RECHKOBLIT,R.E.JOHNSON,A.BUKU,L.PRAKASH,S.PRAKASH, JRNL AUTH 2 A.K.AGGARWAL JRNL TITL STRUCTURAL INSIGHTS INTO MUTAGENICITY OF ANTICANCER JRNL TITL 2 NUCLEOSIDE ANALOG CYTARABINE DURING REPLICATION BY DNA JRNL TITL 3 POLYMERASE ETA. JRNL REF SCI REP V. 9 16400 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 31704958 JRNL DOI 10.1038/S41598-019-52703-7 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17623 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 894 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.5310 - 4.3509 1.00 2849 143 0.1775 0.2155 REMARK 3 2 4.3509 - 3.4539 1.00 2801 147 0.1480 0.1769 REMARK 3 3 3.4539 - 3.0175 1.00 2786 153 0.1699 0.2110 REMARK 3 4 3.0175 - 2.7416 1.00 2791 135 0.1823 0.2188 REMARK 3 5 2.7416 - 2.5452 1.00 2744 156 0.2024 0.2592 REMARK 3 6 2.5452 - 2.3951 1.00 2758 160 0.2121 0.2970 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.92 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 : 0.011 3872 REMARK 3 ANGLE : 0.828 5312 REMARK 3 CHIRALITY : 0.044 601 REMARK 3 PLANARITY : 0.004 617 REMARK 3 DIHEDRAL : 20.928 2274 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 6PZ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243325. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-13 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 : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.100 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R CDTE 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17653 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.395 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.10 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.50 REMARK 200 R MERGE FOR SHELL (I) : 0.91000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES BUFFER, PEG1500, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING 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 27.11600 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 54.23200 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 40.67400 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 67.79000 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 13.55800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 HIS A 0 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 MET A 1 CG SD CE REMARK 470 THR A 3 OG1 CG2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 LEU A 132 CG CD1 CD2 REMARK 470 GLN A 133 CG CD OE1 NE2 REMARK 470 GLN A 135 CG CD OE1 NE2 REMARK 470 THR A 155 OG1 CG2 REMARK 470 GLU A 159 CG CD OE1 OE2 REMARK 470 THR A 160 CG2 REMARK 470 GLN A 179 CG CD OE1 NE2 REMARK 470 ASP A 181 CG OD1 OD2 REMARK 470 ASN A 182 CG OD1 ND2 REMARK 470 LEU A 183 CG CD1 CD2 REMARK 470 GLU A 268 CG CD OE1 OE2 REMARK 470 GLU A 292 CD OE1 OE2 REMARK 470 LYS A 328 CG CD CE NZ REMARK 470 ARG A 334 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 335 CG CD OE1 OE2 REMARK 470 LYS A 354 CE NZ REMARK 470 LYS A 376 CG CD CE NZ REMARK 470 LEU A 378 CG CD1 CD2 REMARK 470 LEU A 381 CD1 CD2 REMARK 470 LYS A 404 CE NZ REMARK 470 ASN A 405 CG OD1 ND2 REMARK 470 ILE A 411 CG1 CG2 CD1 REMARK 470 GLN A 412 CG CD OE1 NE2 REMARK 470 THR A 413 OG1 CG2 REMARK 470 LYS A 428 CE NZ REMARK 470 DC T 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DC T 1 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC T 1 C6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ALA A 332 H TRP A 415 1.38 REMARK 500 O ALA A 332 N TRP A 415 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HH21 ARG A 253 OD1 ASP A 360 4564 1.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DT T 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 CYS A 16 66.37 29.14 REMARK 500 TYR A 39 94.64 68.89 REMARK 500 SER A 62 32.19 74.15 REMARK 500 ASN A 182 92.59 67.28 REMARK 500 SER A 217 -159.10 -161.13 REMARK 500 SER A 257 -4.53 90.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 MET A 14 O 81.2 REMARK 620 3 ASP A 115 OD1 90.8 78.5 REMARK 620 4 XG4 A 501 O1A 109.5 169.2 99.4 REMARK 620 5 XG4 A 501 O1B 157.7 80.9 98.6 88.9 REMARK 620 6 XG4 A 501 O1G 81.7 93.8 170.1 89.3 86.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 ASP A 115 OD2 116.1 REMARK 620 3 GLU A 116 OE2 73.8 104.3 REMARK 620 4 XG4 A 501 O1A 104.0 97.1 157.2 REMARK 620 5 HOH A 615 O 76.4 167.4 79.9 77.6 REMARK 620 6 DT P 8 O3' 161.2 67.7 87.3 93.5 101.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XG4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 504 DBREF 6PZ3 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 6PZ3 P 1 8 PDB 6PZ3 6PZ3 1 8 DBREF 6PZ3 T 1 12 PDB 6PZ3 6PZ3 1 12 SEQADV 6PZ3 GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 6PZ3 PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 6PZ3 HIS A 0 UNP Q9Y253 EXPRESSION TAG SEQADV 6PZ3 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 P 8 DA DG DC DA DC DT DG DT SEQRES 1 T 12 DC DA DT CAR DA DC DA DG DT DG DC DT HET CAR T 4 31 HET XG4 A 501 46 HET MG A 502 1 HET MG A 503 1 HET GOL A 504 14 HETNAM CAR CYTOSINE ARABINOSE-5'-PHOSPHATE HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CAR C9 H14 N3 O8 P FORMUL 4 XG4 C10 H17 N6 O12 P3 FORMUL 5 MG 2(MG 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *123(H2 O) HELIX 1 AA1 CYS A 16 ASN A 26 1 11 HELIX 2 AA2 PRO A 27 ARG A 30 5 4 HELIX 3 AA3 SER A 51 ALA A 56 1 6 HELIX 4 AA4 TRP A 64 CYS A 72 1 9 HELIX 5 AA5 LEU A 89 ARG A 105 1 17 HELIX 6 AA6 LEU A 121 LYS A 131 1 11 HELIX 7 AA7 SER A 138 LEU A 142 5 5 HELIX 8 AA8 GLN A 162 LEU A 178 1 17 HELIX 9 AA9 SER A 185 GLY A 209 1 25 HELIX 10 AB1 ASN A 219 ASN A 230 1 12 HELIX 11 AB2 SER A 239 GLY A 241 5 3 HELIX 12 AB3 SER A 242 GLN A 249 1 8 HELIX 13 AB4 MET A 250 ILE A 255 5 6 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 THR A 333 ASP A 360 1 28 HELIX 20 AC2 ASP A 391 LYS A 404 1 14 HELIX 21 AC3 ASN A 405 ASN A 407 5 3 SHEET 1 AA1 6 VAL A 108 SER A 113 0 SHEET 2 AA1 6 GLU A 116 ASP A 120 -1 O 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 GLY A 46 VAL A 50 0 SHEET 2 AA2 3 CYS A 34 GLN A 38 -1 N VAL A 36 O ALA A 49 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 4 ILE A 319 ASN A 324 0 SHEET 2 AA4 4 LEU A 419 ALA A 431 -1 O ALA A 426 N ILE A 319 SHEET 3 AA4 4 ARG A 361 VAL A 372 -1 N VAL A 367 O CYS A 425 SHEET 4 AA4 4 LEU A 381 ALA A 386 -1 O CYS A 385 N LEU A 366 LINK O3' DT T 3 P CAR T 4 1555 1555 1.61 LINK O3' CAR T 4 P DA T 5 1555 1555 1.59 LINK OD1 ASP A 13 MG MG A 502 1555 1555 1.95 LINK OD2 ASP A 13 MG MG A 503 1555 1555 2.09 LINK O MET A 14 MG MG A 502 1555 1555 2.34 LINK OD1 ASP A 115 MG MG A 502 1555 1555 2.18 LINK OD2 ASP A 115 MG MG A 503 1555 1555 2.14 LINK OE2 GLU A 116 MG MG A 503 1555 1555 1.89 LINK O1A XG4 A 501 MG MG A 502 1555 1555 2.08 LINK O1B XG4 A 501 MG MG A 502 1555 1555 2.00 LINK O1G XG4 A 501 MG MG A 502 1555 1555 2.07 LINK O1A XG4 A 501 MG MG A 503 1555 1555 2.09 LINK MG MG A 503 O HOH A 615 1555 1555 2.11 LINK MG MG A 503 O3' DT P 8 1555 1555 2.47 CISPEP 1 LEU A 150 PRO A 151 0 2.09 CISPEP 2 LYS A 231 PRO A 232 0 2.84 CISPEP 3 SER A 416 PRO A 417 0 -3.53 SITE 1 AC1 21 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC1 21 PHE A 17 PHE A 18 ILE A 48 ALA A 49 SITE 3 AC1 21 TYR A 52 ARG A 55 ARG A 61 ASP A 115 SITE 4 AC1 21 LYS A 231 MG A 502 MG A 503 HOH A 615 SITE 5 AC1 21 HOH A 649 HOH A 655 HOH A 658 DT P 8 SITE 6 AC1 21 CAR T 4 SITE 1 AC2 5 ASP A 13 MET A 14 ASP A 115 XG4 A 501 SITE 2 AC2 5 MG A 503 SITE 1 AC3 7 ASP A 13 ASP A 115 GLU A 116 XG4 A 501 SITE 2 AC3 7 MG A 502 HOH A 615 DT P 8 SITE 1 AC4 8 ARG A 24 PRO A 244 SER A 248 GLY A 276 SITE 2 AC4 8 GLU A 277 HOH A 602 HOH A 605 HOH A 625 CRYST1 98.221 98.221 81.348 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 0.010181 0.005878 0.000000 0.00000 SCALE2 0.000000 0.011756 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012293 0.00000 CONECT 168 7272 CONECT 169 7273 CONECT 177 7272 CONECT 1808 7272 CONECT 1809 7273 CONECT 1822 7273 CONECT 6848 7273 CONECT 6915 6939 CONECT 6939 6915 6940 6941 6942 CONECT 6940 6939 CONECT 6941 6939 CONECT 6942 6939 6943 CONECT 6943 6942 6944 6959 6960 CONECT 6944 6943 6945 6946 6961 CONECT 6945 6944 6950 CONECT 6946 6944 6947 6948 6962 CONECT 6947 6946 6970 CONECT 6948 6946 6949 6950 6963 CONECT 6949 6948 6964 CONECT 6950 6945 6948 6951 6965 CONECT 6951 6950 6952 6958 CONECT 6952 6951 6953 6954 CONECT 6953 6952 CONECT 6954 6952 6955 CONECT 6955 6954 6956 6957 CONECT 6956 6955 6966 6967 CONECT 6957 6955 6958 6968 CONECT 6958 6951 6957 6969 CONECT 6959 6943 CONECT 6960 6943 CONECT 6961 6944 CONECT 6962 6946 CONECT 6963 6948 CONECT 6964 6949 CONECT 6965 6950 CONECT 6966 6956 CONECT 6967 6956 CONECT 6968 6957 CONECT 6969 6958 CONECT 6970 6947 CONECT 7226 7227 7232 7257 CONECT 7227 7226 7228 7229 CONECT 7228 7227 7258 7259 CONECT 7229 7227 7230 CONECT 7230 7229 7231 7236 CONECT 7231 7230 7232 7234 CONECT 7232 7226 7231 7233 CONECT 7233 7232 CONECT 7234 7231 7235 CONECT 7235 7234 7236 7260 CONECT 7236 7230 7235 7240 CONECT 7237 7241 7245 7250 7256 CONECT 7238 7242 7246 7250 7251 CONECT 7239 7243 7247 7251 7252 CONECT 7240 7236 7244 7254 7261 CONECT 7241 7237 7272 7273 CONECT 7242 7238 7272 CONECT 7243 7239 7272 CONECT 7244 7240 7248 7262 7263 CONECT 7245 7237 7264 CONECT 7246 7238 7265 CONECT 7247 7239 CONECT 7248 7244 7249 7253 7266 CONECT 7249 7248 7267 CONECT 7250 7237 7238 7268 CONECT 7251 7238 7239 CONECT 7252 7239 CONECT 7253 7248 7254 7255 7269 CONECT 7254 7240 7253 CONECT 7255 7253 7256 7270 7271 CONECT 7256 7237 7255 CONECT 7257 7226 CONECT 7258 7228 CONECT 7259 7228 CONECT 7260 7235 CONECT 7261 7240 CONECT 7262 7244 CONECT 7263 7244 CONECT 7264 7245 CONECT 7265 7246 CONECT 7266 7248 CONECT 7267 7249 CONECT 7268 7250 CONECT 7269 7253 CONECT 7270 7255 CONECT 7271 7255 CONECT 7272 168 177 1808 7241 CONECT 7272 7242 7243 CONECT 7273 169 1809 1822 6848 CONECT 7273 7241 7302 CONECT 7274 7275 7276 7280 7281 CONECT 7275 7274 7282 CONECT 7276 7274 7277 7278 7283 CONECT 7277 7276 7284 CONECT 7278 7276 7279 7285 7286 CONECT 7279 7278 7287 CONECT 7280 7274 CONECT 7281 7274 CONECT 7282 7275 CONECT 7283 7276 CONECT 7284 7277 CONECT 7285 7278 CONECT 7286 7278 CONECT 7287 7279 CONECT 7302 7273 MASTER 370 0 5 21 15 0 12 6 3824 3 105 36 END