HEADER TRANSFERASE/DNA 31-OCT-14 4RPZ TITLE HUMAN DNA POLYMERASE BETA WITH GAPPED DNA CONTAINING AN 8-OXO-7,8- TITLE 2 DIHYDRO-GUANINE (8-OXOG)AND DCTP SOAKED WITH MGCL2 FOR 60 S 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(P*GP*TP*CP*GP*G)-3'); COMPND 8 CHAIN: D; COMPND 9 SYNONYM: 5-MER PHOSPHORYLATED DOWNSTREAM PRIMER; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3'); COMPND 13 CHAIN: P; COMPND 14 SYNONYM: 10-MER PRIMER; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*(8OG) COMPND 18 P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'); COMPND 19 CHAIN: T; COMPND 20 SYNONYM: 16-MER TEMPLATE; COMPND 21 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: POL B, POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; 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: PET28B; 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; SOURCE 19 MOL_ID: 4; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 22 ORGANISM_TAXID: 32630 KEYWDS X-FAMILY, POL BETA, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.VYAS,A.J.REED,Z.SUO REVDAT 3 28-FEB-24 4RPZ 1 REMARK SEQADV LINK REVDAT 2 06-MAY-15 4RPZ 1 JRNL REVDAT 1 15-APR-15 4RPZ 0 JRNL AUTH R.VYAS,A.J.REED,E.J.TOKARSKY,Z.SUO JRNL TITL VIEWING HUMAN DNA POLYMERASE BETA FAITHFULLY AND JRNL TITL 2 UNFAITHFULLY BYPASS AN OXIDATIVE LESION BY TIME-DEPENDENT JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF J.AM.CHEM.SOC. V. 137 5225 2015 JRNL REFN ISSN 0002-7863 JRNL PMID 25825995 JRNL DOI 10.1021/JACS.5B02109 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 19738 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 + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 974 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1441 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2613 REMARK 3 NUCLEIC ACID ATOMS : 652 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.348 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.239 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.203 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.412 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3534 ; 0.007 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3008 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4859 ; 1.303 ; 1.817 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6973 ; 0.848 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 329 ; 5.862 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;34.887 ;24.127 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 516 ;14.516 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;13.801 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 498 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3413 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 788 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1307 ; 1.360 ; 2.697 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1306 ; 1.360 ; 2.696 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1633 ; 2.392 ; 4.041 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1634 ; 2.391 ; 4.043 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2227 ; 1.360 ; 2.887 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2226 ; 1.359 ; 2.887 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3224 ; 2.247 ; 4.304 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4297 ; 4.025 ;23.369 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4267 ; 3.974 ;23.358 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4RPZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000087652. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20173 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 44.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.12200 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) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.54800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 350 MM SODIUM REMARK 280 ACETATE, 17% PEG3350, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K 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 39.66000 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: 7910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -145.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, 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 MET A -1 REMARK 465 GLY A 0 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 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 REMARK 465 HIS A 341 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 DG D 1 P DG D 1 OP3 -0.127 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 ALA A 32 77.83 -115.89 REMARK 500 CYS A 178 -140.16 -113.06 REMARK 500 SER A 204 130.08 -173.60 REMARK 500 ASP A 246 13.28 48.09 REMARK 500 THR A 304 0.20 92.69 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 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 93.1 REMARK 620 3 VAL A 65 O 86.6 106.2 REMARK 620 4 HOH A 589 O 96.0 69.7 175.1 REMARK 620 5 DC D 3 OP1 164.3 102.6 88.1 90.3 REMARK 620 6 HOH D 202 O 86.9 163.9 89.9 94.3 78.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 94.8 REMARK 620 3 ILE A 106 O 88.6 93.0 REMARK 620 4 HOH A 517 O 83.0 86.3 171.5 REMARK 620 5 DG P 9 OP1 162.5 100.2 99.7 88.8 REMARK 620 6 HOH P 208 O 75.4 161.1 71.0 108.0 92.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 190 OD1 46.4 REMARK 620 3 ASP A 192 OD1 102.2 82.5 REMARK 620 4 ASP A 256 OD2 80.0 122.6 92.3 REMARK 620 5 DCP A 410 O2A 109.8 68.4 90.6 168.9 REMARK 620 6 DC P 10 O3' 159.3 154.1 88.3 81.8 87.7 REMARK 620 7 DC P 10 O3' 146.8 135.5 110.9 99.8 69.2 29.7 REMARK 620 8 DC P 11 OP1 108.5 67.8 92.4 169.1 2.0 88.6 69.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 91.0 REMARK 620 3 PPV A 409 O11 171.9 93.8 REMARK 620 4 PPV A 409 O22 96.5 171.3 78.3 REMARK 620 5 DCP A 410 O1B 172.5 81.8 14.8 90.8 REMARK 620 6 DCP A 410 O2A 86.9 78.4 100.4 106.3 89.4 REMARK 620 7 DCP A 410 O3G 98.3 169.5 77.6 9.4 88.7 97.1 REMARK 620 8 HOH A 610 O 97.1 90.8 76.4 83.9 85.3 168.6 92.9 REMARK 620 9 DC P 11 OP1 86.4 80.4 100.8 104.4 90.2 2.1 95.2 170.6 REMARK 620 N 1 2 3 4 5 6 7 8 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 ASP A 318 OD1 REMARK 620 2 ASP A 321 OD2 112.0 REMARK 620 3 HOH A 593 O 60.7 100.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG P 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PPV A 409 O31 REMARK 620 2 DCP A 410 O1A 79.3 REMARK 620 3 DCP A 410 O3A 8.7 72.2 REMARK 620 4 HOH A 613 O 114.0 145.8 117.0 REMARK 620 5 HOH A 619 O 85.7 76.2 79.3 73.7 REMARK 620 6 HOH A 621 O 152.7 85.8 144.5 68.3 68.4 REMARK 620 7 DC P 11 OP2 79.2 2.3 72.3 147.9 78.5 86.8 REMARK 620 8 HOH P 210 O 95.2 91.0 100.1 117.4 166.8 107.9 88.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DCP D 101 O1B REMARK 620 2 DCP D 101 O2G 88.5 REMARK 620 3 HOH D 208 O 83.6 63.9 REMARK 620 4 HOH D 209 O 101.6 137.1 157.8 REMARK 620 5 HOH D 210 O 144.1 75.9 60.5 112.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA 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 CL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL 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 PPV A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG P 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RPX RELATED DB: PDB REMARK 900 RELATED ID: 4RPY RELATED DB: PDB REMARK 900 RELATED ID: 4RQ0 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ1 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ2 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ3 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ4 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ5 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ6 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ7 RELATED DB: PDB REMARK 900 RELATED ID: 4RQ8 RELATED DB: PDB DBREF 4RPZ A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4RPZ D 1 5 PDB 4RPZ 4RPZ 1 5 DBREF 4RPZ P 1 11 PDB 4RPZ 4RPZ 1 11 DBREF 4RPZ T 1 16 PDB 4RPZ 4RPZ 1 16 SEQADV 4RPZ MET A -1 UNP P06746 EXPRESSION TAG SEQADV 4RPZ GLY A 0 UNP P06746 EXPRESSION TAG SEQADV 4RPZ HIS A 336 UNP P06746 EXPRESSION TAG SEQADV 4RPZ HIS A 337 UNP P06746 EXPRESSION TAG SEQADV 4RPZ HIS A 338 UNP P06746 EXPRESSION TAG SEQADV 4RPZ HIS A 339 UNP P06746 EXPRESSION TAG SEQADV 4RPZ HIS A 340 UNP P06746 EXPRESSION TAG SEQADV 4RPZ HIS A 341 UNP P06746 EXPRESSION TAG SEQRES 1 A 343 MET GLY MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU SEQRES 2 A 343 ASN GLY GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN SEQRES 3 A 343 PHE GLU LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN SEQRES 4 A 343 ALA TYR ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO SEQRES 5 A 343 HIS LYS ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO SEQRES 6 A 343 GLY VAL GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE SEQRES 7 A 343 LEU ALA THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG SEQRES 8 A 343 GLN ASP ASP THR SER SER SER ILE ASN PHE LEU THR ARG SEQRES 9 A 343 VAL SER GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL SEQRES 10 A 343 ASP GLU GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN SEQRES 11 A 343 GLU ASP LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS SEQRES 12 A 343 TYR PHE GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU SEQRES 13 A 343 MET LEU GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS SEQRES 14 A 343 LYS VAL ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER SEQRES 15 A 343 PHE ARG ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL SEQRES 16 A 343 LEU LEU THR HIS PRO SER PHE THR SER GLU SER THR LYS SEQRES 17 A 343 GLN PRO LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN SEQRES 18 A 343 LYS VAL HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU SEQRES 19 A 343 THR LYS PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN SEQRES 20 A 343 ASP GLU LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG SEQRES 21 A 343 LEU ILE PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR SEQRES 22 A 343 PHE THR GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA SEQRES 23 A 343 HIS ALA LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR SEQRES 24 A 343 ILE ARG PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO SEQRES 25 A 343 LEU PRO VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE SEQRES 26 A 343 GLN TRP LYS TYR ARG GLU PRO LYS ASP ARG SER GLU HIS SEQRES 27 A 343 HIS HIS HIS HIS HIS SEQRES 1 D 5 DG DT DC DG DG SEQRES 1 P 11 DG DC DT DG DA DT DG DC DG DC DC SEQRES 1 T 16 DC DC DG DA DC 8OG DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC MODRES 4RPZ 8OG T 6 DG HET 8OG T 6 23 HET MG A 401 1 HET MG A 402 1 HET NA A 403 1 HET NA A 404 1 HET NA A 405 1 HET CL A 406 1 HET CL A 407 1 HET CL A 408 1 HET PPV A 409 9 HET DCP A 410 28 HET DCP D 101 28 HET NA D 102 1 HET MG P 101 1 HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PPV PYROPHOSPHATE HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE FORMUL 4 8OG C10 H14 N5 O8 P FORMUL 5 MG 3(MG 2+) FORMUL 7 NA 4(NA 1+) FORMUL 10 CL 3(CL 1-) FORMUL 13 PPV H4 O7 P2 FORMUL 14 DCP 2(C9 H16 N3 O13 P3) FORMUL 18 HOH *158(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 TYR A 49 1 18 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 ASP A 91 THR A 101 1 11 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 ASN A 128 1 8 HELIX 9 9 GLU A 129 LEU A 132 5 4 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 GLU A 147 1 6 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 CYS A 178 ARG A 183 1 6 HELIX 14 14 LYS A 209 VAL A 221 1 13 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 GLY A 274 1 11 HELIX 17 17 SER A 275 LYS A 289 1 15 HELIX 18 18 SER A 315 ILE A 323 1 9 HELIX 19 19 GLU A 329 SER A 334 5 6 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 VAL A 177 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ASP A 256 N VAL A 193 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236 SHEET 1 C 2 PHE A 200 THR A 201 0 SHEET 2 C 2 SER A 204 THR A 205 -1 O SER A 204 N THR A 201 SHEET 1 D 2 PHE A 291 ILE A 293 0 SHEET 2 D 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DC T 5 P 8OG T 6 1555 1555 1.60 LINK O3' 8OG T 6 P DG T 7 1555 1555 1.60 LINK O LYS A 60 NA NA A 403 1555 1555 2.28 LINK O LEU A 62 NA NA A 403 1555 1555 2.25 LINK O VAL A 65 NA NA A 403 1555 1555 2.24 LINK O THR A 101 NA NA A 404 1555 1555 2.22 LINK O VAL A 103 NA NA A 404 1555 1555 2.26 LINK O ILE A 106 NA NA A 404 1555 1555 2.25 LINK OD2 ASP A 190 MG MG A 401 1555 1555 2.18 LINK OD1 ASP A 190 MG MG A 401 1555 1555 2.98 LINK OD1 ASP A 190 MG MG A 402 1555 1555 2.15 LINK OD1 ASP A 192 MG MG A 401 1555 1555 2.16 LINK OD2 ASP A 192 MG MG A 402 1555 1555 2.23 LINK OD2 ASP A 256 MG MG A 401 1555 1555 2.19 LINK OD1 ASP A 318 NA NA A 405 1555 1555 2.26 LINK OD2 ASP A 321 NA NA A 405 1555 1555 2.27 LINK MG MG A 401 O2ABDCP A 410 1555 1555 2.18 LINK MG MG A 401 O3'B DC P 10 1555 1555 2.19 LINK MG MG A 401 O3'A DC P 10 1555 1555 2.19 LINK MG MG A 401 OP1A DC P 11 1555 1555 2.20 LINK MG MG A 402 O11APPV A 409 1555 1555 2.17 LINK MG MG A 402 O22APPV A 409 1555 1555 2.19 LINK MG MG A 402 O1BBDCP A 410 1555 1555 2.17 LINK MG MG A 402 O2ABDCP A 410 1555 1555 2.18 LINK MG MG A 402 O3GBDCP A 410 1555 1555 2.18 LINK MG MG A 402 O HOH A 610 1555 1555 2.17 LINK MG MG A 402 OP1A DC P 11 1555 1555 2.18 LINK NA NA A 403 O HOH A 589 1555 1555 2.25 LINK NA NA A 403 OP1 DC D 3 1555 1555 2.29 LINK NA NA A 403 O HOH D 202 1555 1555 2.25 LINK NA NA A 404 O HOH A 517 1555 1555 2.25 LINK NA NA A 404 OP1 DG P 9 1555 1555 2.24 LINK NA NA A 404 O HOH P 208 1555 1555 2.25 LINK NA NA A 405 O HOH A 593 1555 1555 2.24 LINK O31APPV A 409 MG MG P 101 1555 1555 2.19 LINK O1ABDCP A 410 MG MG P 101 1555 1555 2.17 LINK O3ABDCP A 410 MG MG P 101 1555 1555 2.17 LINK O HOH A 613 MG MG P 101 1555 1555 2.17 LINK O HOH A 619 MG MG P 101 1555 1555 2.18 LINK O HOH A 621 MG MG P 101 1555 1555 2.17 LINK O1B DCP D 101 NA NA D 102 1555 1555 2.05 LINK O2G DCP D 101 NA NA D 102 1555 1555 2.23 LINK NA NA D 102 O HOH D 208 1555 1555 2.33 LINK NA NA D 102 O HOH D 209 1555 1555 2.23 LINK NA NA D 102 O HOH D 210 1555 1555 2.97 LINK OP2A DC P 11 MG MG P 101 1555 1555 2.18 LINK MG MG P 101 O HOH P 210 1555 1555 2.18 CISPEP 1 GLY A 274 SER A 275 0 2.00 SITE 1 AC1 7 ASP A 190 ASP A 192 ASP A 256 MG A 402 SITE 2 AC1 7 DCP A 410 DC P 10 DC P 11 SITE 1 AC2 7 ASP A 190 ASP A 192 MG A 401 PPV A 409 SITE 2 AC2 7 DCP A 410 HOH A 610 DC P 11 SITE 1 AC3 6 LYS A 60 LEU A 62 VAL A 65 HOH A 589 SITE 2 AC3 6 DC D 3 HOH D 202 SITE 1 AC4 6 THR A 101 VAL A 103 ILE A 106 HOH A 517 SITE 2 AC4 6 DG P 9 HOH P 208 SITE 1 AC5 4 ASP A 318 ASP A 321 HOH A 593 DCP D 101 SITE 1 AC6 4 GLN A 264 TYR A 266 CYS A 267 HOH A 561 SITE 1 AC7 4 ASN A 294 THR A 297 ARG A 299 HOH A 563 SITE 1 AC8 3 ALA A 32 HIS A 34 LYS A 35 SITE 1 AC9 14 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC9 14 GLY A 189 ASP A 190 ASP A 192 MG A 402 SITE 3 AC9 14 HOH A 610 HOH A 613 HOH A 619 HOH A 620 SITE 4 AC9 14 DC P 11 MG P 101 SITE 1 BC1 25 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 BC1 25 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 BC1 25 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 BC1 25 ASN A 279 MG A 401 MG A 402 HOH A 610 SITE 5 BC1 25 HOH A 613 HOH A 619 HOH A 620 HOH A 621 SITE 6 BC1 25 DC P 10 MG P 101 HOH P 209 HOH P 210 SITE 7 BC1 25 8OG T 6 SITE 1 BC2 16 ASP A 124 LYS A 127 TYR A 266 ASP A 314 SITE 2 BC2 16 SER A 315 LYS A 317 ASP A 318 ASP A 321 SITE 3 BC2 16 NA A 405 HOH A 585 HOH A 593 DG D 4 SITE 4 BC2 16 DG D 5 NA D 102 HOH D 208 DC T 2 SITE 1 BC3 6 ASP A 124 LYS A 127 DCP D 101 HOH D 208 SITE 2 BC3 6 HOH D 209 HOH D 210 SITE 1 BC4 7 PPV A 409 DCP A 410 HOH A 613 HOH A 619 SITE 2 BC4 7 HOH A 621 DC P 11 HOH P 210 CRYST1 49.410 79.320 55.410 90.00 106.20 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 0.020239 0.000000 0.005880 0.00000 SCALE2 0.000000 0.012607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018794 0.00000