HEADER TRANSFERASE/DNA 15-OCT-19 6UOL TITLE Y271G DNA POLYMERASE BETA SUBSTRATE COMPLEX WITH A TEMPLATING CYTOSINE TITLE 2 AND INCOMING RGTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 3 3'); COMPND 4 CHAIN: T; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'); COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA POLYMERASE BETA; COMPND 16 CHAIN: A; COMPND 17 EC: 2.7.7.7,4.2.99.-; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: POLB; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE, RIBONUCLEOTIDE, OXIDIZED NUCLEOTIDE, DNA DAMAGE, DNA KEYWDS 2 BINDING PROTEIN, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SMITH,B.D.FREUDENTHAL REVDAT 4 11-OCT-23 6UOL 1 LINK REVDAT 3 19-FEB-20 6UOL 1 JRNL REVDAT 2 15-JAN-20 6UOL 1 JRNL REVDAT 1 08-JAN-20 6UOL 0 JRNL AUTH M.R.SMITH,K.S.ALNAJJAR,N.M.HOITSMA,J.B.SWEASY, JRNL AUTH 2 B.D.FREUDENTHAL JRNL TITL MOLECULAR AND STRUCTURAL CHARACTERIZATION OF OXIDIZED JRNL TITL 2 RIBONUCLEOTIDE INSERTION INTO DNA BY HUMAN DNA POLYMERASE JRNL TITL 3 BETA. JRNL REF J.BIOL.CHEM. V. 295 1613 2020 JRNL REFN ESSN 1083-351X JRNL PMID 31892517 JRNL DOI 10.1074/JBC.RA119.011569 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 67.8 REMARK 3 NUMBER OF REFLECTIONS : 42206 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.910 REMARK 3 FREE R VALUE TEST SET COUNT : 4183 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 25.0880 - 5.9885 0.98 1842 201 0.1367 0.1594 REMARK 3 2 5.9885 - 4.7639 1.00 1845 210 0.1309 0.2044 REMARK 3 3 4.7639 - 4.1648 0.99 1862 203 0.1261 0.1902 REMARK 3 4 4.1648 - 3.7854 0.99 1856 188 0.1295 0.1981 REMARK 3 5 3.7854 - 3.5149 1.00 1875 185 0.1467 0.2219 REMARK 3 6 3.5149 - 3.3081 0.99 1888 185 0.1635 0.2412 REMARK 3 7 3.3081 - 3.1428 0.99 1849 203 0.1919 0.2299 REMARK 3 8 3.1428 - 3.0062 0.99 1835 209 0.2312 0.2750 REMARK 3 9 3.0062 - 2.8907 0.98 1851 202 0.2343 0.3162 REMARK 3 10 2.8907 - 2.7910 0.97 1777 229 0.2438 0.3388 REMARK 3 11 2.7910 - 2.7039 0.93 1759 184 0.2463 0.3001 REMARK 3 12 2.7039 - 2.6267 0.86 1597 176 0.2240 0.3026 REMARK 3 13 2.6267 - 2.5576 0.77 1445 157 0.2354 0.3036 REMARK 3 14 2.5576 - 2.4953 0.70 1310 137 0.2405 0.2608 REMARK 3 15 2.4953 - 2.4386 0.64 1199 113 0.2343 0.3435 REMARK 3 16 2.4386 - 2.3867 0.59 1103 137 0.2362 0.2745 REMARK 3 17 2.3867 - 2.3390 0.56 1057 124 0.2312 0.2976 REMARK 3 18 2.3390 - 2.2949 0.53 993 120 0.2491 0.3072 REMARK 3 19 2.2949 - 2.2539 0.52 948 112 0.2425 0.2728 REMARK 3 20 2.2539 - 2.2158 0.51 917 102 0.2404 0.2866 REMARK 3 21 2.2158 - 2.1800 0.51 972 113 0.2524 0.3227 REMARK 3 22 2.1800 - 2.1465 0.50 957 97 0.2441 0.2985 REMARK 3 23 2.1465 - 2.1150 0.50 918 101 0.2389 0.2704 REMARK 3 24 2.1150 - 2.0852 0.49 923 119 0.2491 0.3173 REMARK 3 25 2.0852 - 2.0570 0.46 837 90 0.2529 0.3267 REMARK 3 26 2.0570 - 2.0303 0.42 774 76 0.2570 0.3282 REMARK 3 27 2.0303 - 2.0050 0.36 680 82 0.2659 0.3276 REMARK 3 28 2.0050 - 1.9808 0.32 584 65 0.2686 0.3188 REMARK 3 29 1.9808 - 1.9578 0.23 423 47 0.2908 0.3515 REMARK 3 30 1.9578 - 1.9360 0.08 147 16 0.3015 0.3259 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.21 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6UOL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000243469. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R 200K-A REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42206 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.936 REMARK 200 RESOLUTION RANGE LOW (A) : 25.088 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.86400 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: 2FMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG3350, 0.35 M SODIUM ACETATE, REMARK 280 0.05 M IMIDAZOLE, PH 8.0., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 40.20000 REMARK 290 SMTRY3 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, D, A 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 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 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 127 CG CD CE NZ REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 ASN A 245 CG OD1 ND2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 VAL A 303 CG1 CG2 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 LYS A 120 10.23 -144.96 REMARK 500 CYS A 178 -134.41 -110.98 REMARK 500 LYS A 230 117.94 -162.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 645 DISTANCE = 5.87 ANGSTROMS 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 NA A 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 HOH P 104 O 91.9 REMARK 620 3 THR A 101 O 174.2 83.5 REMARK 620 4 VAL A 103 O 92.5 168.4 92.7 REMARK 620 5 ILE A 106 O 94.3 84.1 88.7 84.9 REMARK 620 6 HOH A 624 O 94.5 95.1 82.5 95.2 171.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH P 117 O REMARK 620 2 HOH A 605 O 69.3 REMARK 620 3 HOH A 641 O 77.1 89.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 407 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC D 3 OP1 REMARK 620 2 HOH D 103 O 74.3 REMARK 620 3 LYS A 60 O 172.0 97.7 REMARK 620 4 LEU A 62 O 94.3 168.2 93.6 REMARK 620 5 VAL A 65 O 89.0 88.4 91.5 94.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 404 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 105 O REMARK 620 2 HOH D 108 O 81.5 REMARK 620 3 ASP A 145 OD2 169.0 87.5 REMARK 620 4 HIS A 252 ND1 101.0 175.2 90.0 REMARK 620 5 HOH A 577 O 93.2 85.0 85.5 90.7 REMARK 620 6 HOH A 634 O 80.6 83.0 98.5 101.4 167.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 410 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 94.9 REMARK 620 3 GTP A 409 O1G 86.4 173.3 REMARK 620 4 GTP A 409 O1B 171.2 92.9 85.4 REMARK 620 5 GTP A 409 O1A 93.7 94.6 91.9 89.8 REMARK 620 6 HOH A 555 O 91.7 79.2 94.2 85.6 172.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 411 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 192 OD1 132.6 REMARK 620 3 GTP A 409 O1A 78.9 92.2 REMARK 620 4 HOH A 511 O 109.1 116.1 117.1 REMARK 620 5 HOH A 614 O 76.1 90.1 147.9 90.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 222 CE1 REMARK 620 2 HIS A 222 NE2 29.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 285 ND1 REMARK 620 2 GLU A 288 OE1 82.0 REMARK 620 3 HOH A 643 O 153.5 112.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 411 DBREF 6UOL T 1 16 PDB 6UOL 6UOL 1 16 DBREF 6UOL P 1 10 PDB 6UOL 6UOL 1 10 DBREF 6UOL D 1 5 PDB 6UOL 6UOL 1 5 DBREF 6UOL A 1 335 UNP P06746 DPOLB_HUMAN 1 335 SEQADV 6UOL GLY A 271 UNP P06746 TYR 271 ENGINEERED MUTATION SEQRES 1 T 16 DC DC DG DA DC DC DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DOC SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU GLY PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU HET DOC P 10 18 HET EDO A 401 10 HET MN A 402 1 HET MN A 403 1 HET MN A 404 1 HET NA A 405 1 HET NA A 406 1 HET NA A 407 1 HET CL A 408 1 HET GTP A 409 32 HET MN A 410 1 HET MN A 411 1 HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 DOC C9 H14 N3 O6 P FORMUL 5 EDO C2 H6 O2 FORMUL 6 MN 5(MN 2+) FORMUL 9 NA 3(NA 1+) FORMUL 12 CL CL 1- FORMUL 13 GTP C10 H16 N5 O14 P3 FORMUL 16 HOH *203(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 TYR A 49 1 18 HELIX 3 AA3 SER A 55 LYS A 61 1 7 HELIX 4 AA4 GLY A 66 GLY A 80 1 15 HELIX 5 AA5 LEU A 82 ASP A 91 1 10 HELIX 6 AA6 ASP A 91 THR A 101 1 11 HELIX 7 AA7 GLY A 107 GLU A 117 1 11 HELIX 8 AA8 THR A 121 ASN A 128 1 8 HELIX 9 AA9 GLU A 129 LEU A 132 5 4 HELIX 10 AB1 ASN A 133 TYR A 142 1 10 HELIX 11 AB2 TYR A 142 LYS A 148 1 7 HELIX 12 AB3 ARG A 152 ASP A 170 1 19 HELIX 13 AB4 CYS A 178 ARG A 183 1 6 HELIX 14 AB5 LEU A 211 VAL A 221 1 11 HELIX 15 AB6 PRO A 261 ASP A 263 5 3 HELIX 16 AB7 GLN A 264 GLY A 274 1 11 HELIX 17 AB8 SER A 275 LYS A 289 1 15 HELIX 18 AB9 SER A 315 ILE A 323 1 9 HELIX 19 AC1 GLU A 329 ARG A 333 5 5 SHEET 1 AA1 2 ILE A 150 PRO A 151 0 SHEET 2 AA1 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 AA2 5 ILE A 174 VAL A 177 0 SHEET 2 AA2 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236 SHEET 1 AA3 2 PHE A 200 THR A 201 0 SHEET 2 AA3 2 SER A 204 THR A 205 -1 O SER A 204 N THR A 201 SHEET 1 AA4 2 PHE A 291 ILE A 293 0 SHEET 2 AA4 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DG P 9 P DOC P 10 1555 1555 1.60 LINK OP1 DG P 9 NA NA A 406 1555 1555 2.37 LINK O HOH P 104 NA NA A 406 1555 1555 2.39 LINK O HOH P 117 NA NA A 405 1555 1555 2.26 LINK OP1 DC D 3 NA NA A 407 1555 1555 2.58 LINK O HOH D 103 NA NA A 407 1555 1555 2.80 LINK O HOH D 105 MN MN A 404 1556 1555 2.33 LINK O HOH D 108 MN MN A 404 1556 1555 2.44 LINK O LYS A 60 NA NA A 407 1555 1555 2.44 LINK O LEU A 62 NA NA A 407 1555 1555 2.37 LINK O VAL A 65 NA NA A 407 1555 1555 2.41 LINK O THR A 101 NA NA A 406 1555 1555 2.26 LINK O VAL A 103 NA NA A 406 1555 1555 2.56 LINK O ILE A 106 NA NA A 406 1555 1555 2.60 LINK OD2 ASP A 145 MN MN A 404 1555 1555 2.12 LINK OD1 ASP A 190 MN MN A 410 1555 1555 2.15 LINK OD2 ASP A 190 MN MN A 411 1555 1555 2.39 LINK OD2 ASP A 192 MN MN A 410 1555 1555 2.12 LINK OD1 ASP A 192 MN MN A 411 1555 1555 2.14 LINK CE1 HIS A 222 MN MN A 403 1555 1555 2.65 LINK NE2 HIS A 222 MN MN A 403 1555 1555 2.30 LINK ND1 HIS A 252 MN MN A 404 1555 1555 2.35 LINK ND1 HIS A 285 MN MN A 402 1555 1555 2.27 LINK OE1 GLU A 288 MN MN A 402 1555 1555 2.72 LINK MN MN A 402 O HOH A 643 1555 1555 2.58 LINK MN MN A 404 O HOH A 577 1555 1555 2.51 LINK MN MN A 404 O HOH A 634 1555 1555 2.53 LINK NA NA A 405 O HOH A 605 1555 1555 2.23 LINK NA NA A 405 O HOH A 641 1555 1555 2.50 LINK NA NA A 406 O HOH A 624 1555 1555 2.41 LINK O1G GTP A 409 MN MN A 410 1555 1555 2.11 LINK O1B GTP A 409 MN MN A 410 1555 1555 2.05 LINK O1A GTP A 409 MN MN A 410 1555 1555 2.19 LINK O1A GTP A 409 MN MN A 411 1555 1555 2.45 LINK MN MN A 410 O HOH A 555 1555 1555 2.18 LINK MN MN A 411 O HOH A 511 1555 1555 2.04 LINK MN MN A 411 O HOH A 614 1555 1555 2.56 CISPEP 1 GLY A 274 SER A 275 0 4.69 SITE 1 AC1 4 ARG A 149 GLU A 154 PRO A 251 ARG A 253 SITE 1 AC2 3 HIS A 285 GLU A 288 HOH A 643 SITE 1 AC3 1 HIS A 222 SITE 1 AC4 6 ASP A 145 HIS A 252 HOH A 577 HOH A 634 SITE 2 AC4 6 HOH D 105 HOH D 108 SITE 1 AC5 3 HOH A 605 HOH A 641 HOH P 117 SITE 1 AC6 6 THR A 101 VAL A 103 ILE A 106 HOH A 624 SITE 2 AC6 6 DG P 9 HOH P 104 SITE 1 AC7 5 LYS A 60 LEU A 62 VAL A 65 DC D 3 SITE 2 AC7 5 HOH D 103 SITE 1 AC8 4 ALA A 32 ILE A 33 HIS A 34 LYS A 35 SITE 1 AC9 27 GLY A 179 SER A 180 ARG A 183 SER A 188 SITE 2 AC9 27 GLY A 189 ASP A 190 ASP A 192 GLY A 271 SITE 3 AC9 27 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 AC9 27 ASN A 279 ARG A 283 MN A 410 MN A 411 SITE 5 AC9 27 HOH A 503 HOH A 546 HOH A 554 HOH A 555 SITE 6 AC9 27 HOH A 576 HOH A 597 HOH A 605 HOH A 608 SITE 7 AC9 27 DOC P 10 DC T 6 DG T 7 SITE 1 AD1 5 ASP A 190 ASP A 192 GTP A 409 MN A 411 SITE 2 AD1 5 HOH A 555 SITE 1 AD2 6 ASP A 190 ASP A 192 GTP A 409 MN A 410 SITE 2 AD2 6 HOH A 511 HOH A 614 CRYST1 50.800 80.400 55.500 90.00 107.90 90.00 P 1 21 1 2 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 0.019685 0.000000 0.006358 0.00000 SCALE2 0.000000 0.012438 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018935 0.00000