HEADER HYDROLASE, LYASE/DNA 31-JUL-17 5WN5 TITLE APE1 EXONUCLEASE SUBSTRATE COMPLEX WITH A C/T MISMATCH AND MN2+ 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 BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HYDROLASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,A.M.WHITAKER REVDAT 3 04-OCT-23 5WN5 1 LINK REVDAT 2 18-DEC-19 5WN5 1 REMARK REVDAT 1 28-FEB-18 5WN5 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 74865 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3790 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 24.7366 - 6.5567 0.99 2732 148 0.1615 0.1817 REMARK 3 2 6.5567 - 5.2203 1.00 2741 142 0.1612 0.1680 REMARK 3 3 5.2203 - 4.5651 0.99 2693 146 0.1477 0.2016 REMARK 3 4 4.5651 - 4.1498 0.98 2698 139 0.1480 0.1678 REMARK 3 5 4.1498 - 3.8536 0.97 2655 143 0.1763 0.2122 REMARK 3 6 3.8536 - 3.6271 0.99 2737 154 0.1836 0.2205 REMARK 3 7 3.6271 - 3.4460 0.99 2723 136 0.1936 0.2150 REMARK 3 8 3.4460 - 3.2963 0.99 2688 158 0.2157 0.2813 REMARK 3 9 3.2963 - 3.1697 0.96 2683 131 0.2344 0.2589 REMARK 3 10 3.1697 - 3.0605 0.94 2570 140 0.2508 0.2321 REMARK 3 11 3.0605 - 2.9650 0.91 2489 135 0.2922 0.3773 REMARK 3 12 2.9650 - 2.8804 0.91 2499 129 0.3088 0.2741 REMARK 3 13 2.8804 - 2.8046 0.94 2549 146 0.2896 0.4035 REMARK 3 14 2.8046 - 2.7363 0.95 2622 133 0.2740 0.3026 REMARK 3 15 2.7363 - 2.6742 0.96 2621 142 0.2806 0.3321 REMARK 3 16 2.6742 - 2.6173 0.98 2704 155 0.2904 0.3478 REMARK 3 17 2.6173 - 2.5650 0.98 2730 124 0.3014 0.3793 REMARK 3 18 2.5650 - 2.5167 0.99 2732 136 0.2865 0.3648 REMARK 3 19 2.5167 - 2.4718 0.98 2627 152 0.2800 0.3774 REMARK 3 20 2.4718 - 2.4299 0.99 2743 146 0.2910 0.3405 REMARK 3 21 2.4299 - 2.3907 0.99 2644 147 0.3092 0.3420 REMARK 3 22 2.3907 - 2.3540 0.98 2720 156 0.3085 0.3618 REMARK 3 23 2.3540 - 2.3194 0.97 2731 139 0.3372 0.4355 REMARK 3 24 2.3194 - 2.2868 0.96 2576 143 0.4479 0.5019 REMARK 3 25 2.2868 - 2.2559 0.94 2659 127 0.3967 0.5069 REMARK 3 26 2.2559 - 2.2266 0.87 2354 125 0.5983 0.5819 REMARK 3 27 2.2266 - 2.1988 0.78 2155 118 0.5547 0.6075 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.69 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 : 0.008 5499 REMARK 3 ANGLE : 1.039 7634 REMARK 3 CHIRALITY : 0.053 814 REMARK 3 PLANARITY : 0.006 834 REMARK 3 DIHEDRAL : 20.329 3151 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 5WN5 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_1000229072. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-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 : 74865 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.69800 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 (%): 53.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 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 32.22200 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: 5070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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: 500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 GLU A 149 REMARK 465 GLU A 150 REMARK 465 SER A 201 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 77 CG CD CE NZ REMARK 470 ASP A 124 CG OD1 OD2 REMARK 470 LYS A 125 CG CD CE NZ REMARK 470 ASP A 152 CG OD1 OD2 REMARK 470 GLN A 153 CG CD OE1 NE2 REMARK 470 LYS A 224 CG CD CE NZ REMARK 470 LYS B 103 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 470 ASN B 272 CG OD1 ND2 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 D 2 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG D 9 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 DG D 9 C3' - O3' - P ANGL. DEV. = 11.2 DEGREES REMARK 500 DG E 1 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC E 21 O4' - C1' - N1 ANGL. DEV. = 3.0 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 LYS A 79 33.85 76.78 REMARK 500 SER A 129 -145.51 46.39 REMARK 500 SER A 129 -143.94 43.88 REMARK 500 LYS B 79 31.08 70.99 REMARK 500 CYS B 99 118.78 -165.62 REMARK 500 LEU B 111 71.11 -163.10 REMARK 500 ASP B 124 34.43 -157.16 REMARK 500 SER B 129 -143.64 56.24 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 MN B 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 207 O REMARK 620 2 ASP B 70 OD1 101.8 REMARK 620 3 GLU B 96 OE2 86.0 103.8 REMARK 620 N 1 2 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 70 OD1 REMARK 620 2 GLU A 96 OE2 71.8 REMARK 620 N 1 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 ASP A 283 O REMARK 620 2 HOH A 526 O 111.6 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 402 DBREF 5WN5 C 1 11 PDB 5WN5 5WN5 1 11 DBREF 5WN5 D 1 10 PDB 5WN5 5WN5 1 10 DBREF 5WN5 E 1 21 PDB 5WN5 5WN5 1 21 DBREF 5WN5 A 43 318 UNP P27695 APEX1_HUMAN 43 318 DBREF 5WN5 B 43 318 UNP P27695 APEX1_HUMAN 43 318 SEQADV 5WN5 ALA A 138 UNP P27695 CYS 138 ENGINEERED MUTATION SEQADV 5WN5 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 MN E 101 1 HET NA A 401 1 HET MN A 402 1 HET EDO A 403 4 HET MN B 401 1 HET EDO B 402 4 HETNAM C7R 2'-DEOXY-5'-O-THIOPHOSPHONOCYTIDINE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL 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 MN 3(MN 2+) FORMUL 7 NA NA 1+ FORMUL 9 EDO 2(C2 H6 O2) FORMUL 12 HOH *159(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 GLY A 176 VAL A 180 5 5 HELIX 6 AA6 ARG A 181 ALA A 200 1 20 HELIX 7 AA7 GLU A 216 LEU A 220 5 5 HELIX 8 AA8 PRO A 223 LYS A 227 5 5 HELIX 9 AA9 THR A 233 VAL A 247 1 15 HELIX 10 AB1 SER A 252 TYR A 257 1 6 HELIX 11 AB2 TYR A 269 MET A 271 5 3 HELIX 12 AB3 ASN A 272 ASN A 277 1 6 HELIX 13 AB4 HIS A 289 PRO A 293 5 5 HELIX 14 AB5 GLY B 71 LYS B 78 1 8 HELIX 15 AB6 LYS B 79 ALA B 88 1 10 HELIX 16 AB7 PRO B 105 GLN B 109 5 5 HELIX 17 AB8 ASP B 148 ASP B 152 5 5 HELIX 18 AB9 GLY B 176 VAL B 180 5 5 HELIX 19 AC1 ARG B 181 SER B 201 1 21 HELIX 20 AC2 GLU B 216 LEU B 220 5 5 HELIX 21 AC3 PRO B 223 LYS B 227 5 5 HELIX 22 AC4 THR B 233 VAL B 247 1 15 HELIX 23 AC5 SER B 252 TYR B 257 1 6 HELIX 24 AC6 TYR B 269 ASN B 277 5 9 HELIX 25 AC7 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 CYS A 93 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 GLU A 161 N LYS A 141 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 VAL B 131 N SER B 120 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 CYS B 93 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 1.64 LINK O3'B DG D 9 P BC7R D 10 1555 1555 1.60 LINK O HOH D 207 MN MN B 401 1555 1555 2.53 LINK OD1 ASP A 70 MN MN A 402 1555 1555 1.74 LINK OE2 GLU A 96 MN MN A 402 1555 1555 2.78 LINK O ASP A 283 NA NA A 401 1555 1555 2.95 LINK NA NA A 401 O HOH A 526 1555 1555 2.99 LINK OD1 ASP B 70 MN MN B 401 1555 1555 1.86 LINK OE2 GLU B 96 MN MN B 401 1555 1555 2.65 CISPEP 1 VAL A 247 PRO A 248 0 -11.45 CISPEP 2 VAL B 247 PRO B 248 0 -5.84 SITE 1 AC1 2 DC E 6 DG E 7 SITE 1 AC2 4 PHE A 253 ARG A 281 ASP A 283 HOH A 526 SITE 1 AC3 2 ASP A 70 GLU A 96 SITE 1 AC4 4 LEU A 44 TYR A 45 ASN A 277 SER A 302 SITE 1 AC5 4 ASP B 70 GLU B 96 C7R D 10 HOH D 207 SITE 1 AC6 4 LEU B 44 TYR B 45 ARG B 274 ASN B 277 CRYST1 71.503 64.444 91.522 90.00 109.93 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 0.013985 0.000000 0.005071 0.00000 SCALE2 0.000000 0.015517 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011623 0.00000