HEADER HYDROLASE, LYASE/DNA 31-JUL-17 5WN4 TITLE APE1 EXONUCLEASE SUBSTRATE COMPLEX WITH A C/T MISMATCH COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'); COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DV3))-3'); COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'- COMPND 11 D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 12 3'); COMPND 13 CHAIN: E; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 17 CHAIN: A, B; COMPND 18 SYNONYM: APEX1, APEX NUCLEASE,APEN,APURINIC-APYRIMIDINIC ENDONUCLEASE COMPND 19 1, APE-1, REF-1, REDOX FACTOR-1; COMPND 20 EC: 3.1.-.-, 4.2.99.18; COMPND 21 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: APEX1, APE, APE1, APEX, APX, HAP1, REF1; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,A.M.WHITAKER REVDAT 3 04-OCT-23 5WN4 1 REMARK REVDAT 2 27-NOV-19 5WN4 1 REMARK REVDAT 1 28-FEB-18 5WN4 0 JRNL AUTH A.M.WHITAKER,T.S.FLYNN,B.D.FREUDENTHAL JRNL TITL MOLECULAR SNAPSHOTS OF APE1 PROOFREADING MISMATCHES AND JRNL TITL 2 REMOVING DNA DAMAGE. JRNL REF NAT COMMUN V. 9 399 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29374164 JRNL DOI 10.1038/S41467-017-02175-Y REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.4 REMARK 3 NUMBER OF REFLECTIONS : 71157 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.690 REMARK 3 FREE R VALUE TEST SET COUNT : 3334 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 24.5641 - 6.0207 0.98 3454 158 0.1592 0.2271 REMARK 3 2 6.0207 - 4.7905 0.99 3455 176 0.1589 0.2352 REMARK 3 3 4.7905 - 4.1883 0.94 3311 163 0.1447 0.1560 REMARK 3 4 4.1883 - 3.8069 0.91 3215 156 0.1652 0.1707 REMARK 3 5 3.8069 - 3.5349 0.90 3186 160 0.1852 0.2163 REMARK 3 6 3.5349 - 3.3270 0.88 3110 157 0.1966 0.2070 REMARK 3 7 3.3270 - 3.1607 0.86 3025 156 0.2182 0.2637 REMARK 3 8 3.1607 - 3.0234 0.84 2942 147 0.2408 0.2624 REMARK 3 9 3.0234 - 2.9072 0.81 2825 159 0.2713 0.3647 REMARK 3 10 2.9072 - 2.8070 0.81 2887 130 0.2900 0.3188 REMARK 3 11 2.8070 - 2.7194 0.79 2774 135 0.2790 0.3301 REMARK 3 12 2.7194 - 2.6417 0.77 2663 144 0.2749 0.3656 REMARK 3 13 2.6417 - 2.5723 0.77 2737 120 0.2832 0.3537 REMARK 3 14 2.5723 - 2.5096 0.77 2716 113 0.2731 0.3841 REMARK 3 15 2.5096 - 2.4526 0.75 2623 132 0.2660 0.3129 REMARK 3 16 2.4526 - 2.4004 0.76 2670 145 0.2769 0.3806 REMARK 3 17 2.4004 - 2.3525 0.76 2652 126 0.2903 0.3502 REMARK 3 18 2.3525 - 2.3081 0.75 2629 122 0.2931 0.3923 REMARK 3 19 2.3081 - 2.2669 0.73 2564 118 0.3068 0.3858 REMARK 3 20 2.2669 - 2.2285 0.73 2568 132 0.2902 0.3646 REMARK 3 21 2.2285 - 2.1926 0.73 2596 130 0.2982 0.3918 REMARK 3 22 2.1926 - 2.1589 0.70 2456 132 0.3116 0.3284 REMARK 3 23 2.1589 - 2.1271 0.72 2530 115 0.3045 0.3660 REMARK 3 24 2.1271 - 2.0972 0.64 2235 108 0.3073 0.3538 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.30 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 : 0.009 5581 REMARK 3 ANGLE : 1.065 7760 REMARK 3 CHIRALITY : 0.057 827 REMARK 3 PLANARITY : 0.006 840 REMARK 3 DIHEDRAL : 21.132 3195 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 5WN4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1000228941. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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 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 : 71157 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 95.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.70300 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: PDB ENTRY 5DFF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7% PEG20000, 100 MM SODIUM CITRATE, REMARK 280 15% GLYCEROL, 5 MM CALCIUM CHLORIDE, PH 5.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, 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 31.92250 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 4960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, E, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ASP A 124 CG OD1 OD2 REMARK 470 LYS A 125 CG CD CE NZ REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 GLN B 109 CG CD OE1 NE2 REMARK 470 GLU B 110 CG CD OE1 OE2 REMARK 470 ASP B 124 CG OD1 OD2 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 DT D 3 O3' DT D 3 C3' -0.044 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 D 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG E 1 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT E 4 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC E 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA E 16 O4' - C1' - N9 ANGL. DEV. = 2.3 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 70 75.72 46.43 REMARK 500 LYS A 79 28.25 80.94 REMARK 500 LEU A 114 56.73 -145.00 REMARK 500 SER A 129 -141.91 50.13 REMARK 500 PHE A 232 25.39 -140.74 REMARK 500 CYS B 99 116.88 -160.49 REMARK 500 LEU B 111 54.00 -159.88 REMARK 500 ASP B 124 54.88 -152.53 REMARK 500 LYS B 125 89.24 -163.77 REMARK 500 SER B 129 -137.70 59.61 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 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 66 OG REMARK 620 2 GLN A 95 OE1 83.9 REMARK 620 3 ASP A 283 OD1 153.3 109.0 REMARK 620 4 HOH A 535 O 131.7 113.0 65.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 401 DBREF 5WN4 C 1 11 PDB 5WN4 5WN4 1 11 DBREF 5WN4 D 1 10 PDB 5WN4 5WN4 1 10 DBREF 5WN4 E 1 21 PDB 5WN4 5WN4 1 21 DBREF 5WN4 A 43 318 UNP P27695 APEX1_HUMAN 43 318 DBREF 5WN4 B 43 318 UNP P27695 APEX1_HUMAN 43 318 SEQADV 5WN4 ALA A 138 UNP P27695 CYS 138 ENGINEERED MUTATION SEQADV 5WN4 ALA B 138 UNP P27695 CYS 138 ENGINEERED MUTATION SEQRES 1 C 11 DT DC DG DA DC DG DG DA DT DC DC SEQRES 1 D 10 DG DC DT DG DA DT DG DC DG C7R SEQRES 1 E 21 DG DG DA DT DC DC DG DT DC DG DA DT DC SEQRES 2 E 21 DG DC DA DT DC DA DG DC SEQRES 1 A 276 ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS THR SER PRO SEQRES 2 A 276 SER GLY LYS PRO ALA THR LEU LYS ILE CYS SER TRP ASN SEQRES 3 A 276 VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS LYS GLY LEU SEQRES 4 A 276 ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE LEU CYS LEU SEQRES 5 A 276 GLN GLU THR LYS CYS SER GLU ASN LYS LEU PRO ALA GLU SEQRES 6 A 276 LEU GLN GLU LEU PRO GLY LEU SER HIS GLN TYR TRP SER SEQRES 7 A 276 ALA PRO SER ASP LYS GLU GLY TYR SER GLY VAL GLY LEU SEQRES 8 A 276 LEU SER ARG GLN ALA PRO LEU LYS VAL SER TYR GLY ILE SEQRES 9 A 276 GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG VAL ILE VAL SEQRES 10 A 276 ALA GLU PHE ASP SER PHE VAL LEU VAL THR ALA TYR VAL SEQRES 11 A 276 PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU GLU TYR ARG SEQRES 12 A 276 GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE LEU LYS GLY SEQRES 13 A 276 LEU ALA SER ARG LYS PRO LEU VAL LEU CYS GLY ASP LEU SEQRES 14 A 276 ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG ASN PRO LYS SEQRES 15 A 276 GLY ASN LYS LYS ASN ALA GLY PHE THR PRO GLN GLU ARG SEQRES 16 A 276 GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL PRO LEU ALA SEQRES 17 A 276 ASP SER PHE ARG HIS LEU TYR PRO ASN THR PRO TYR ALA SEQRES 18 A 276 TYR THR PHE TRP THR TYR MET MET ASN ALA ARG SER LYS SEQRES 19 A 276 ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU LEU SER HIS SEQRES 20 A 276 SER LEU LEU PRO ALA LEU CYS ASP SER LYS ILE ARG SER SEQRES 21 A 276 LYS ALA LEU GLY SER ASP HIS CYS PRO ILE THR LEU TYR SEQRES 22 A 276 LEU ALA LEU SEQRES 1 B 276 ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS THR SER PRO SEQRES 2 B 276 SER GLY LYS PRO ALA THR LEU LYS ILE CYS SER TRP ASN SEQRES 3 B 276 VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS LYS GLY LEU SEQRES 4 B 276 ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE LEU CYS LEU SEQRES 5 B 276 GLN GLU THR LYS CYS SER GLU ASN LYS LEU PRO ALA GLU SEQRES 6 B 276 LEU GLN GLU LEU PRO GLY LEU SER HIS GLN TYR TRP SER SEQRES 7 B 276 ALA PRO SER ASP LYS GLU GLY TYR SER GLY VAL GLY LEU SEQRES 8 B 276 LEU SER ARG GLN ALA PRO LEU LYS VAL SER TYR GLY ILE SEQRES 9 B 276 GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG VAL ILE VAL SEQRES 10 B 276 ALA GLU PHE ASP SER PHE VAL LEU VAL THR ALA TYR VAL SEQRES 11 B 276 PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU GLU TYR ARG SEQRES 12 B 276 GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE LEU LYS GLY SEQRES 13 B 276 LEU ALA SER ARG LYS PRO LEU VAL LEU CYS GLY ASP LEU SEQRES 14 B 276 ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG ASN PRO LYS SEQRES 15 B 276 GLY ASN LYS LYS ASN ALA GLY PHE THR PRO GLN GLU ARG SEQRES 16 B 276 GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL PRO LEU ALA SEQRES 17 B 276 ASP SER PHE ARG HIS LEU TYR PRO ASN THR PRO TYR ALA SEQRES 18 B 276 TYR THR PHE TRP THR TYR MET MET ASN ALA ARG SER LYS SEQRES 19 B 276 ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU LEU SER HIS SEQRES 20 B 276 SER LEU LEU PRO ALA LEU CYS ASP SER LYS ILE ARG SER SEQRES 21 B 276 LYS ALA LEU GLY SER ASP HIS CYS PRO ILE THR LEU TYR SEQRES 22 B 276 LEU ALA LEU HET C7R D 10 38 HET NA C 101 1 HET CA D 101 1 HET NA E 101 1 HET EDO A 401 4 HET NA A 402 1 HET CL A 403 1 HET EDO B 401 4 HETNAM C7R 2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE HETNAM NA SODIUM ION HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN C7R 2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE (THIOPHOSPHO HETSYN 2 C7R CONNECTION ISOFORM 1) HETSYN EDO ETHYLENE GLYCOL FORMUL 2 C7R C9 H14 N3 O6 P S FORMUL 6 NA 3(NA 1+) FORMUL 7 CA CA 2+ FORMUL 9 EDO 2(C2 H6 O2) FORMUL 11 CL CL 1- FORMUL 13 HOH *182(H2 O) HELIX 1 AA1 GLY A 71 LYS A 78 1 8 HELIX 2 AA2 LYS A 79 ALA A 88 1 10 HELIX 3 AA3 SER A 100 LEU A 104 5 5 HELIX 4 AA4 PRO A 105 SER A 115 5 11 HELIX 5 AA5 ASP A 148 ASP A 152 5 5 HELIX 6 AA6 GLY A 176 VAL A 180 5 5 HELIX 7 AA7 ARG A 181 LYS A 203 1 23 HELIX 8 AA8 GLU A 216 LEU A 220 5 5 HELIX 9 AA9 PRO A 223 LYS A 227 5 5 HELIX 10 AB1 THR A 233 VAL A 247 1 15 HELIX 11 AB2 SER A 252 TYR A 257 1 6 HELIX 12 AB3 TYR A 269 MET A 271 5 3 HELIX 13 AB4 ASN A 272 ASN A 277 1 6 HELIX 14 AB5 HIS A 289 PRO A 293 5 5 HELIX 15 AB6 GLY B 71 LYS B 78 1 8 HELIX 16 AB7 LYS B 79 ALA B 88 1 10 HELIX 17 AB8 SER B 100 LEU B 104 5 5 HELIX 18 AB9 PRO B 105 GLN B 109 5 5 HELIX 19 AC1 ASP B 148 ASP B 152 5 5 HELIX 20 AC2 GLY B 176 VAL B 180 5 5 HELIX 21 AC3 ARG B 181 SER B 201 1 21 HELIX 22 AC4 GLU B 216 LEU B 220 5 5 HELIX 23 AC5 PRO B 223 LYS B 227 5 5 HELIX 24 AC6 THR B 233 VAL B 247 1 15 HELIX 25 AC7 SER B 252 TYR B 257 1 6 HELIX 26 AC8 TYR B 269 MET B 271 5 3 HELIX 27 AC9 ASN B 272 ASN B 277 1 6 HELIX 28 AD1 HIS B 289 PRO B 293 5 5 SHEET 1 AA1 6 HIS A 116 SER A 120 0 SHEET 2 AA1 6 VAL A 131 SER A 135 -1 O LEU A 133 N TYR A 118 SHEET 3 AA1 6 ILE A 91 GLN A 95 -1 N LEU A 92 O LEU A 134 SHEET 4 AA1 6 LEU A 62 ASN A 68 1 N CYS A 65 O ILE A 91 SHEET 5 AA1 6 ILE A 312 LEU A 316 -1 O LEU A 314 N ILE A 64 SHEET 6 AA1 6 LEU A 295 ILE A 300 -1 N LYS A 299 O THR A 313 SHEET 1 AA2 6 LYS A 141 TYR A 144 0 SHEET 2 AA2 6 VAL A 157 GLU A 161 -1 O VAL A 159 N SER A 143 SHEET 3 AA2 6 VAL A 166 TYR A 171 -1 O LEU A 167 N ALA A 160 SHEET 4 AA2 6 LEU A 205 ASP A 210 1 O VAL A 206 N VAL A 168 SHEET 5 AA2 6 ASP A 283 LEU A 287 -1 O LEU A 286 N LEU A 207 SHEET 6 AA2 6 ALA A 250 ASP A 251 -1 N ALA A 250 O LEU A 287 SHEET 1 AA3 6 HIS B 116 SER B 120 0 SHEET 2 AA3 6 VAL B 131 SER B 135 -1 O SER B 135 N HIS B 116 SHEET 3 AA3 6 ILE B 91 GLN B 95 -1 N LEU B 92 O LEU B 134 SHEET 4 AA3 6 LEU B 62 ASN B 68 1 N CYS B 65 O ILE B 91 SHEET 5 AA3 6 ILE B 312 LEU B 316 -1 O LEU B 314 N ILE B 64 SHEET 6 AA3 6 LEU B 295 ILE B 300 -1 N LYS B 299 O THR B 313 SHEET 1 AA4 6 LYS B 141 TYR B 144 0 SHEET 2 AA4 6 VAL B 157 GLU B 161 -1 O VAL B 159 N SER B 143 SHEET 3 AA4 6 VAL B 166 TYR B 171 -1 O LEU B 167 N ALA B 160 SHEET 4 AA4 6 LEU B 205 ASP B 210 1 O VAL B 206 N VAL B 168 SHEET 5 AA4 6 ASP B 283 LEU B 287 -1 O LEU B 286 N LEU B 207 SHEET 6 AA4 6 ALA B 250 ASP B 251 -1 N ALA B 250 O LEU B 287 LINK O3'A DG D 9 P AC7R D 10 1555 1555 1.62 LINK O3'B DG D 9 P BC7R D 10 1555 1555 1.60 LINK O3' DC C 11 NA NA C 101 1555 1555 2.44 LINK OP2 DC D 8 CA CA D 101 1555 1555 3.08 LINK O5' DG E 1 NA NA E 101 1555 1555 2.76 LINK OG SER A 66 NA NA A 402 1555 1555 2.85 LINK OE1 GLN A 95 NA NA A 402 1555 1555 2.41 LINK OD1 ASP A 283 NA NA A 402 1555 1555 2.84 LINK NA NA A 402 O HOH A 535 1555 1555 2.88 CISPEP 1 VAL A 247 PRO A 248 0 -8.92 CISPEP 2 PRO B 112 GLY B 113 0 0.54 CISPEP 3 VAL B 247 PRO B 248 0 -9.05 SITE 1 AC1 1 DC C 11 SITE 1 AC2 2 DG D 7 DC D 8 SITE 1 AC3 2 PHE A 266 DG E 1 SITE 1 AC4 3 ALA A 60 THR A 61 ASP A 90 SITE 1 AC5 7 SER A 66 TRP A 67 ASN A 68 GLN A 95 SITE 2 AC5 7 GLY A 209 ASP A 283 HOH A 535 SITE 1 AC6 1 ASP A 163 SITE 1 AC7 4 GLU B 161 VAL B 166 LEU B 199 ARG B 202 CRYST1 71.334 63.845 90.924 90.00 109.66 90.00 P 1 21 1 4 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 0.014019 0.000000 0.005007 0.00000 SCALE2 0.000000 0.015663 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011679 0.00000