HEADER DNA BINDING PROTEIN/DNA 21-SEP-21 7S9O TITLE BINARY COMPLEX OF DNA POLYMERASE BETA WITH RING OPEN INTERMEDIATE TITLE 2 FAPY-DG IN THE TEMPLATE POSITION CAVEAT 7S9O 8PI T 6 HAS WRONG CHIRALITY AT ATOM C3' 8PI T 6 HAS WRONG CAVEAT 2 7S9O CHIRALITY AT ATOM C4' 8PI T 6 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 7S9O C5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7,4.2.99.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*C*(IFP) COMPND 8 P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A*(SO4))-3'); COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630; SOURCE 16 MOL_ID: 4; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630 KEYWDS FAPY-DG INTERMEDIATE, POLYMERASE BETA, DNA BINDING PROTEIN-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,B.J.RYAN REVDAT 2 18-OCT-23 7S9O 1 REMARK REVDAT 1 03-AUG-22 7S9O 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. 2.23 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) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 58.0 REMARK 3 NUMBER OF REFLECTIONS : 24619 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2437 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 24.5500 - 5.7000 0.89 2003 227 0.1461 0.2028 REMARK 3 2 5.7000 - 4.5400 0.92 2051 229 0.1506 0.2254 REMARK 3 3 4.5400 - 3.9700 0.94 2092 231 0.1446 0.2482 REMARK 3 4 3.9600 - 3.6000 0.95 2137 231 0.1748 0.2714 REMARK 3 5 3.6000 - 3.3500 0.94 2105 232 0.2037 0.2595 REMARK 3 6 3.3500 - 3.1500 0.90 2029 238 0.2147 0.3130 REMARK 3 7 3.1500 - 2.9900 0.84 1872 190 0.2807 0.3709 REMARK 3 8 2.9900 - 2.8600 0.79 1787 205 0.3023 0.3786 REMARK 3 9 2.8600 - 2.7500 0.69 1561 169 0.3000 0.3173 REMARK 3 10 2.7500 - 2.6600 0.56 1255 144 0.3138 0.3477 REMARK 3 11 2.6600 - 2.5700 0.41 930 89 0.3191 0.4505 REMARK 3 12 2.5700 - 2.5000 0.31 700 72 0.3203 0.3415 REMARK 3 13 2.5000 - 2.4300 0.24 536 60 0.3106 0.4473 REMARK 3 14 2.4300 - 2.3800 0.19 421 44 0.3290 0.3903 REMARK 3 15 2.3800 - 2.3200 0.14 308 33 0.3345 0.4026 REMARK 3 16 2.3200 - 2.2700 0.10 222 24 0.3324 0.4225 REMARK 3 17 2.2700 - 2.2300 0.08 173 19 0.3375 0.4860 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) : 0.345 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.983 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.54 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 : 0.012 3354 REMARK 3 ANGLE : 1.079 4642 REMARK 3 CHIRALITY : 0.066 514 REMARK 3 PLANARITY : 0.007 495 REMARK 3 DIHEDRAL : 25.715 1303 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 7S9O 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_1000259497. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-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 : 24619 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 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 (%) : 95.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 6.05 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: 3ISB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14-19% PEG 3350, 50 MM IMIDAZOLE PH REMARK 280 8.0, 350 MM SODIUM ACETATE, VAPOR DIFFUSION, 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 39.41300 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: 4190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, D 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 THR A 205 REMARK 465 LYS A 206 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 PRO A 7 CG CD REMARK 470 GLN A 8 CG CD OE1 NE2 REMARK 470 GLU A 9 CG CD OE1 OE2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLU A 203 CG CD OE1 OE2 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 ASP A 246 CG OD1 OD2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 LYS A 248 CG CD CE NZ 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 NZ LYS A 317 OD2 ASP A 321 1.70 REMARK 500 O ARG A 89 O HOH A 501 2.15 REMARK 500 N7 DG T 15 O HOH T 101 2.19 REMARK 500 OG SER A 202 OD2 ASP A 263 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DC T 5 O3' 8PI T 6 P -0.091 REMARK 500 DC T 5 O3' 8PI T 6 P -0.245 REMARK 500 8PI T 6 O3' DT T 7 P -0.246 REMARK 500 DA T 14 O3' DA T 14 C3' -0.036 REMARK 500 DG P 9 O3' DG P 9 C3' -0.045 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 DC T 5 C3' - O3' - P ANGL. DEV. = 34.7 DEGREES REMARK 500 DC T 5 C3' - O3' - P ANGL. DEV. = 34.3 DEGREES REMARK 500 8PI T 6 O3' - P - O5' ANGL. DEV. = 12.5 DEGREES REMARK 500 8PI T 6 O3' - P - O5' ANGL. DEV. = 42.6 DEGREES REMARK 500 8PI T 6 O3' - P - OP2 ANGL. DEV. = 19.3 DEGREES REMARK 500 8PI T 6 O3' - P - OP1 ANGL. DEV. = -16.2 DEGREES REMARK 500 8PI T 6 O3' - P - OP1 ANGL. DEV. = -15.1 DEGREES REMARK 500 8PI T 6 C3' - O3' - P ANGL. DEV. = 45.0 DEGREES REMARK 500 8PI T 6 C3' - O3' - P ANGL. DEV. = 54.4 DEGREES REMARK 500 DT T 7 O3' - P - O5' ANGL. DEV. = 11.6 DEGREES REMARK 500 DT T 7 O3' - P - OP2 ANGL. DEV. = -16.0 DEGREES REMARK 500 DT T 7 O3' - P - OP2 ANGL. DEV. = -17.9 DEGREES REMARK 500 DT T 7 O3' - P - OP1 ANGL. DEV. = 8.3 DEGREES REMARK 500 DG D 4 O4' - C1' - N9 ANGL. DEV. = 2.6 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 ASN A 12 37.04 -142.14 REMARK 500 ALA A 32 69.55 -112.75 REMARK 500 ALA A 38 -72.94 -58.85 REMARK 500 LYS A 52 109.09 -51.34 REMARK 500 GLN A 90 58.12 -114.20 REMARK 500 ASN A 128 45.05 -144.26 REMARK 500 CYS A 178 -149.37 -104.72 REMARK 500 PRO A 208 31.69 -83.76 REMARK 500 ASN A 245 -15.04 67.70 REMARK 500 ASP A 246 -55.33 -127.89 REMARK 500 THR A 273 -74.16 -97.90 REMARK 500 GLN A 324 73.62 58.49 REMARK 500 ASP A 332 40.28 -96.99 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 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 85.0 REMARK 620 3 ILE A 106 O 87.3 73.7 REMARK 620 4 DG P 9 OP1 176.0 93.1 88.8 REMARK 620 5 HOH P 105 O 99.0 105.7 173.6 84.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 HOH A 510 O 68.5 REMARK 620 3 HOH A 528 O 100.5 60.6 REMARK 620 4 HOH P 105 O 100.8 167.5 117.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 106 O REMARK 620 2 DG P 9 OP2 83.8 REMARK 620 N 1 DBREF 7S9O A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 7S9O T 1 16 PDB 7S9O 7S9O 1 16 DBREF 7S9O P 1 10 PDB 7S9O 7S9O 1 10 DBREF 7S9O D 1 5 PDB 7S9O 7S9O 1 5 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 SEQRES 1 T 16 DC DC DG DA DC 8PI 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 HET 8PI T 6 46 HET NA A 401 1 HET NA A 402 1 HET NA A 403 1 HETNAM 8PI 1-{[(5S)-2-AMINO-5-FORMAMIDO-6-OXO-5,6- HETNAM 2 8PI DIHYDROPYRIMIDIN-4-YL]AMINO}-1,2-DIDEOXY-5-O- HETNAM 3 8PI PHOSPHONO-D-ERYTHRO-PENTITOL HETNAM NA SODIUM ION FORMUL 2 8PI C10 H18 N5 O8 P FORMUL 5 NA 3(NA 1+) FORMUL 8 HOH *49(H2 O) HELIX 1 AA1 GLN A 8 VAL A 29 1 22 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 GLN A 90 1 9 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 LYS A 127 1 7 HELIX 9 AA9 ASN A 128 LEU A 132 5 5 HELIX 10 AB1 ASN A 133 TYR A 142 1 10 HELIX 11 AB2 TYR A 142 GLU A 147 1 6 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 GLY A 274 1 14 HELIX 16 AB7 SER A 275 LYS A 289 1 15 HELIX 17 AB8 SER A 315 GLN A 324 1 10 HELIX 18 AB9 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 THR A 196 N ILE A 174 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 291 ILE A 293 0 SHEET 2 AA3 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DC T 5 P A8PI T 6 1555 1555 1.52 LINK O3'A8PI T 6 P DT T 7 1555 1555 1.56 LINK O THR A 101 NA NA A 401 1555 1555 2.41 LINK O THR A 101 NA NA A 402 1555 1555 2.83 LINK O VAL A 103 NA NA A 401 1555 1555 2.85 LINK O ILE A 106 NA NA A 401 1555 1555 2.57 LINK O ILE A 106 NA NA A 403 1555 1555 3.18 LINK NA NA A 401 OP1 DG P 9 1555 1555 2.33 LINK NA NA A 401 O HOH P 105 1555 1555 2.83 LINK NA NA A 402 O HOH A 510 1555 1555 2.88 LINK NA NA A 402 O HOH A 528 1555 1555 2.56 LINK NA NA A 402 O HOH P 105 1555 1555 2.35 LINK NA NA A 403 OP2 DG P 9 1555 1555 2.65 CRYST1 53.727 78.826 54.949 90.00 105.89 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 0.018613 0.000000 0.005299 0.00000 SCALE2 0.000000 0.012686 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018922 0.00000