HEADER DNA BINDING PROTEIN/DNA 21-SEP-21 7S9P TITLE TERNARY COMPLEX OF DNA POLYMERASE BETA WITH TEMPLATE FAPY-DG AND AN TITLE 2 INCOMING DCTP ANALOG CAVEAT 7S9P 8NI T 6 HAS WRONG CHIRALITY AT ATOM C5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*(FAP) COMPND 3 P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-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*A)-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 POLYMERASE BETA, FAPY-DG, NON-MUTAGENIC, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,B.J.RYAN,M.R.SMITH REVDAT 2 18-OCT-23 7S9P 1 REMARK REVDAT 1 03-AUG-22 7S9P 0 JRNL AUTH B.J.RYAN,H.YANG,J.H.T.BACURIO,M.R.SMITH,A.K.BASU, JRNL AUTH 2 M.M.GREENBERG,B.D.FREUDENTHAL JRNL TITL STRUCTURAL DYNAMICS OF A COMMON MUTAGENIC OXIDATIVE DNA JRNL TITL 2 LESION IN DUPLEX DNA AND DURING DNA REPLICATION. JRNL REF J.AM.CHEM.SOC. V. 144 8054 2022 JRNL REFN ESSN 1520-5126 JRNL PMID 35499923 JRNL DOI 10.1021/JACS.2C00193 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 73.0 REMARK 3 NUMBER OF REFLECTIONS : 50774 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 5051 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 24.5000 - 5.7500 0.99 2079 228 0.1397 0.1622 REMARK 3 2 5.7300 - 4.5700 1.00 2100 217 0.1371 0.1978 REMARK 3 3 4.5700 - 3.9900 0.99 2057 237 0.1254 0.1821 REMARK 3 4 3.9900 - 3.6300 0.99 2081 206 0.1391 0.1597 REMARK 3 5 3.6300 - 3.3700 0.99 2084 212 0.1409 0.1895 REMARK 3 6 3.3700 - 3.1700 0.99 2076 217 0.1584 0.2170 REMARK 3 7 3.1700 - 3.0100 0.98 2040 237 0.1912 0.2400 REMARK 3 8 3.0100 - 2.8800 0.96 2036 219 0.2050 0.2597 REMARK 3 9 2.8800 - 2.7700 0.97 1951 245 0.2007 0.2614 REMARK 3 10 2.7700 - 2.6800 0.96 2015 217 0.2171 0.2652 REMARK 3 11 2.6800 - 2.5900 0.96 2040 207 0.2077 0.2842 REMARK 3 12 2.5900 - 2.5200 0.95 1960 223 0.2088 0.2703 REMARK 3 13 2.5200 - 2.4500 0.92 1953 205 0.2143 0.2841 REMARK 3 14 2.4500 - 2.3900 0.86 1781 200 0.2108 0.2905 REMARK 3 15 2.3900 - 2.3400 0.83 1723 219 0.2161 0.2692 REMARK 3 16 2.3400 - 2.2900 0.78 1612 191 0.2046 0.2525 REMARK 3 17 2.2900 - 2.2400 0.75 1564 186 0.1908 0.2755 REMARK 3 18 2.2400 - 2.2000 0.70 1412 154 0.2066 0.2241 REMARK 3 19 2.2000 - 2.1600 0.67 1421 165 0.2044 0.2920 REMARK 3 20 2.1600 - 2.1200 0.64 1329 146 0.2100 0.2397 REMARK 3 21 2.1200 - 2.0900 0.60 1232 138 0.2146 0.2510 REMARK 3 22 2.0900 - 2.0600 0.56 1159 136 0.2203 0.2674 REMARK 3 23 2.0600 - 2.0300 0.53 1123 105 0.2283 0.2617 REMARK 3 24 2.0300 - 2.0000 0.49 1020 112 0.2340 0.2831 REMARK 3 25 2.0000 - 1.9700 0.46 965 105 0.2462 0.2995 REMARK 3 26 1.9700 - 1.9500 0.39 795 88 0.2605 0.3263 REMARK 3 27 1.9500 - 1.9200 0.33 701 79 0.3216 0.4140 REMARK 3 28 1.9200 - 1.9000 0.28 575 64 0.3242 0.3143 REMARK 3 29 1.9000 - 1.8800 0.23 483 54 0.3660 0.4158 REMARK 3 30 1.8800 - 1.8600 0.17 356 39 0.4218 0.4609 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.226 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.277 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.77 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 : 0.014 3428 REMARK 3 ANGLE : 1.293 4767 REMARK 3 CHIRALITY : 0.076 521 REMARK 3 PLANARITY : 0.007 511 REMARK 3 DIHEDRAL : 25.575 1339 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 7S9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1000259500. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50774 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 5.71 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 1.17.1_3660 REMARK 200 STARTING MODEL: 2FMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14-19% PEG 3350, 50 MM IMIDAZOLE PH REMARK 280 8.0, 350 MM SODIUM ACETATE, 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 39.81050 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: 5630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 87 CD CE NZ REMARK 470 LYS A 120 CD CE NZ REMARK 470 LYS A 127 CG CD CE NZ REMARK 470 LYS A 209 CD CE NZ REMARK 470 LYS A 244 CG CD CE NZ 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: 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 HOH A 590 O HOH A 767 1.70 REMARK 500 OG1 THR A 93 O HOH A 501 2.13 REMARK 500 O HOH A 731 O HOH A 782 2.18 REMARK 500 O HOH A 818 O HOH A 834 2.18 REMARK 500 O HOH A 779 O HOH A 826 2.19 REMARK 500 OD1 ASP A 116 O HOH A 502 2.19 REMARK 500 OP2 DG P 7 O HOH P 101 2.19 REMARK 500 O HOH A 556 O HOH A 600 2.19 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 DG P 9 O4' - C1' - N9 ANGL. DEV. = 2.4 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 ASP A 170 119.58 -163.09 REMARK 500 CYS A 178 -139.33 -115.36 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 NA A 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 HOH P 105 O 88.7 REMARK 620 3 THR A 101 O 164.4 79.1 REMARK 620 4 VAL A 103 O 95.7 174.5 96.0 REMARK 620 5 ILE A 106 O 95.6 93.7 94.9 89.2 REMARK 620 6 HOH A 760 O 90.9 91.0 79.7 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 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA P 10 O3' REMARK 620 2 ASP A 190 OD2 166.8 REMARK 620 3 ASP A 192 OD1 84.5 104.4 REMARK 620 4 ASP A 256 OD2 77.7 91.5 95.8 REMARK 620 5 ASP A 256 OD2 86.7 87.0 71.3 27.0 REMARK 620 6 XC5 A 401 O2A 94.7 95.0 90.7 169.4 161.7 REMARK 620 7 HOH A 559 O 88.7 83.1 171.9 87.0 112.8 85.4 REMARK 620 N 1 2 3 4 5 6 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 DC D 3 OP1 REMARK 620 2 HOH D 106 O 77.2 REMARK 620 3 LYS A 60 O 170.3 94.9 REMARK 620 4 LEU A 62 O 90.9 167.7 97.2 REMARK 620 5 VAL A 65 O 82.3 90.8 92.4 90.8 REMARK 620 6 HOH A 763 O 88.8 89.7 96.8 86.8 170.7 REMARK 620 N 1 2 3 4 5 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 111 O REMARK 620 2 HOH D 112 O 72.5 REMARK 620 3 ASP A 145 OD2 166.8 94.6 REMARK 620 4 HIS A 252 ND1 100.7 171.0 91.8 REMARK 620 5 HOH A 657 O 85.5 82.0 89.8 91.7 REMARK 620 6 HOH A 775 O 87.4 81.5 93.6 104.5 163.3 REMARK 620 N 1 2 3 4 5 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 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 100.6 REMARK 620 3 XC5 A 401 O2A 94.5 87.3 REMARK 620 4 XC5 A 401 O2B 170.2 88.4 89.6 REMARK 620 5 XC5 A 401 O1G 86.2 171.6 97.1 84.5 REMARK 620 6 HOH A 554 O 83.2 87.9 174.2 93.6 88.1 REMARK 620 N 1 2 3 4 5 DBREF 7S9P T 1 16 PDB 7S9P 7S9P 1 16 DBREF 7S9P P 1 10 PDB 7S9P 7S9P 1 10 DBREF 7S9P D 1 5 PDB 7S9P 7S9P 1 5 DBREF 7S9P A 1 335 UNP P06746 DPOLB_HUMAN 1 335 SEQRES 1 T 16 DC DC DG DA DC 8NI DT 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 DA 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 TYR 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 8NI T 6 23 HET XC5 A 401 28 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 CL A 407 1 HET CL A 408 1 HETNAM 8NI N-[(5S)-2-AMINO-5-FORMAMIDO-6-OXO-5,6-DIHYDROPYRIMIDIN- HETNAM 2 8NI 4-YL]-2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 3 8NI PENTOFURANOSYLAMINE HETNAM XC5 2'-DEOXY-5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 XC5 PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 1 8NI C10 H16 N5 O8 P FORMUL 5 XC5 C10 H18 N3 O12 P3 FORMUL 6 MN 3(MN 2+) FORMUL 9 NA 2(NA 1+) FORMUL 11 CL 2(CL 1-) FORMUL 13 HOH *433(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 LYS A 48 1 17 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 LYS A 209 VAL A 221 1 13 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 SER A 334 5 6 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 SER A 229 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' DC T 5 P 8NI T 6 1555 1555 1.59 LINK O3' 8NI T 6 P DT T 7 1555 1555 1.59 LINK OP1 DG P 9 NA NA A 406 1555 1555 2.44 LINK O3' DA P 10 MN MN A 403 1555 1555 2.28 LINK O HOH P 105 NA NA A 406 1555 1555 2.56 LINK OP1 DC D 3 NA NA A 405 1555 1555 2.68 LINK O HOH D 106 NA NA A 405 1555 1555 2.62 LINK O HOH D 111 MN MN A 404 1556 1555 2.54 LINK O HOH D 112 MN MN A 404 1556 1555 2.43 LINK O LYS A 60 NA NA A 405 1555 1555 2.35 LINK O LEU A 62 NA NA A 405 1555 1555 2.46 LINK O VAL A 65 NA NA A 405 1555 1555 2.39 LINK O THR A 101 NA NA A 406 1555 1555 2.32 LINK O VAL A 103 NA NA A 406 1555 1555 2.44 LINK O ILE A 106 NA NA A 406 1555 1555 2.39 LINK OD2 ASP A 145 MN MN A 404 1555 1555 2.11 LINK OD1 ASP A 190 MN MN A 402 1555 1555 1.98 LINK OD2 ASP A 190 MN MN A 403 1555 1555 2.04 LINK OD2 ASP A 192 MN MN A 402 1555 1555 2.10 LINK OD1 ASP A 192 MN MN A 403 1555 1555 2.14 LINK ND1 HIS A 252 MN MN A 404 1555 1555 2.57 LINK OD2BASP A 256 MN MN A 403 1555 1555 2.21 LINK OD2CASP A 256 MN MN A 403 1555 1555 2.32 LINK O2A XC5 A 401 MN MN A 402 1555 1555 2.16 LINK O2B XC5 A 401 MN MN A 402 1555 1555 2.05 LINK O1G XC5 A 401 MN MN A 402 1555 1555 2.16 LINK O2A XC5 A 401 MN MN A 403 1555 1555 2.16 LINK MN MN A 402 O HOH A 554 1555 1555 2.29 LINK MN MN A 403 O HOH A 559 1555 1555 2.26 LINK MN MN A 404 O HOH A 657 1555 1555 2.34 LINK MN MN A 404 O HOH A 775 1555 1555 2.55 LINK NA NA A 405 O HOH A 763 1555 1555 2.37 LINK NA NA A 406 O HOH A 760 1555 1555 2.66 CISPEP 1 GLY A 274 SER A 275 0 3.73 CRYST1 50.673 79.621 55.347 90.00 108.02 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 0.019734 0.000000 0.006420 0.00000 SCALE2 0.000000 0.012560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019000 0.00000