PDB Short entry for 5WN2 HEADER HYDROLASE, LYASE/DNA 31-JUL-17 5WN2 TITLE APE1 EXONUCLEASE SUBSTRATE COMPLEX WITH PHOSPHOGLYCOLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: APEX1, APEX NUCLEASE,APEN,APURINIC-APYRIMIDINIC ENDONUCLEASE COMPND 5 1, APE-1, REF-1, REDOX FACTOR-1; COMPND 6 EC: 3.1.-.-, 4.2.99.18; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*G)-3'); COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'- COMPND 18 D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 19 3'); COMPND 20 CHAIN: E; 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: APEX1, APE, APE1, APEX, APX, HAP1, REF1; 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 HYDROLASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,A.M.WHITAKER REVDAT 2 27-NOV-19 5WN2 1 REMARK REVDAT 1 28-FEB-18 5WN2 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. 2.29 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 34783 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.780 REMARK 3 FREE R VALUE TEST SET COUNT : 3757 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 24.6852 - 6.8172 0.99 2389 142 0.1478 0.1765 REMARK 3 2 6.8172 - 5.4299 1.00 2377 144 0.1606 0.1881 REMARK 3 3 5.4299 - 4.7491 0.99 2355 158 0.1563 0.2206 REMARK 3 4 4.7491 - 4.3174 0.99 2397 149 0.1336 0.1910 REMARK 3 5 4.3174 - 4.0094 1.00 2381 141 0.1480 0.2050 REMARK 3 6 4.0094 - 3.7738 0.99 2382 150 0.1650 0.2797 REMARK 3 7 3.7738 - 3.5854 0.99 2350 128 0.1697 0.2508 REMARK 3 8 3.5854 - 3.4298 0.98 2351 153 0.1779 0.1961 REMARK 3 9 3.4298 - 3.2981 0.97 2360 156 0.2003 0.2419 REMARK 3 10 3.2981 - 3.1845 0.97 2287 133 0.1960 0.2067 REMARK 3 11 3.1845 - 3.0851 0.97 2309 149 0.2006 0.2261 REMARK 3 12 3.0851 - 2.9971 0.96 2360 127 0.2185 0.2906 REMARK 3 13 2.9971 - 2.9183 0.96 2243 167 0.2358 0.2727 REMARK 3 14 2.9183 - 2.8472 0.95 2277 114 0.2407 0.2410 REMARK 3 15 2.8472 - 2.7826 0.95 2291 141 0.2283 0.3195 REMARK 3 16 2.7826 - 2.7234 0.95 2250 144 0.2250 0.2935 REMARK 3 17 2.7234 - 2.6690 0.94 2236 148 0.2254 0.2489 REMARK 3 18 2.6690 - 2.6187 0.94 2242 146 0.2344 0.2873 REMARK 3 19 2.6187 - 2.5720 0.94 2248 132 0.2396 0.2840 REMARK 3 20 2.5720 - 2.5284 0.94 2253 138 0.2437 0.2921 REMARK 3 21 2.5284 - 2.4877 0.93 2273 116 0.2401 0.3259 REMARK 3 22 2.4877 - 2.4495 0.92 2200 135 0.2431 0.3088 REMARK 3 23 2.4495 - 2.4135 0.93 2214 136 0.2609 0.2800 REMARK 3 24 2.4135 - 2.3795 0.92 2126 142 0.2625 0.3543 REMARK 3 25 2.3795 - 2.3474 0.92 2263 126 0.2621 0.2981 REMARK 3 26 2.3474 - 2.3169 0.92 2235 140 0.2722 0.3202 REMARK 3 27 2.3169 - 2.2880 0.67 1578 102 0.2777 0.3501 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.66 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 5508 REMARK 3 ANGLE : 1.126 7638 REMARK 3 CHIRALITY : 0.060 818 REMARK 3 PLANARITY : 0.007 838 REMARK 3 DIHEDRAL : 20.500 3144 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 5WN2 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_1000228910. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-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 : 34821 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 : 4.500 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.59800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 53.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 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 32.15500 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: 4890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D, E 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: 570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLN B 51 CG CD OE1 NE2 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 LYS B 125 CG CD CE NZ REMARK 470 ARG B 202 CG CD NE CZ NH1 NH2 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 OD1 ASP B 219 NH2 ARG B 254 1.15 REMARK 500 O5' DG D 1 O HOH D 201 2.06 REMARK 500 O HOH A 555 O HOH A 583 2.06 REMARK 500 OD1 ASP A 70 O HOH A 501 2.14 REMARK 500 CG ASP B 219 NH2 ARG B 254 2.17 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 C 5 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG D 4 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG D 9 O4' - C1' - N9 ANGL. DEV. = 1.9 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 SER A 56 4.18 -66.76 REMARK 500 LYS A 79 28.26 82.06 REMARK 500 SER A 129 -140.28 45.44 REMARK 500 PHE A 232 29.16 -142.53 REMARK 500 LYS B 79 13.44 80.09 REMARK 500 CYS B 99 114.53 -162.03 REMARK 500 GLU B 110 55.13 -106.10 REMARK 500 SER B 129 -137.02 52.70 REMARK 500 SER B 129 -137.86 54.32 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 CA E 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC E 21 O3' REMARK 620 2 HOH E 209 O 80.4 REMARK 620 3 HOH B 579 O 96.7 81.0 REMARK 620 4 HOH B 501 O 100.7 137.9 139.3 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 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGA D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA E 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA E 103 DBREF 5WN2 A 43 318 UNP P27695 APEX1_HUMAN 43 318 DBREF 5WN2 B 43 318 UNP P27695 APEX1_HUMAN 43 318 DBREF 5WN2 C 1 11 PDB 5WN2 5WN2 1 11 DBREF 5WN2 D 1 9 PDB 5WN2 5WN2 1 9 DBREF 5WN2 E 1 21 PDB 5WN2 5WN2 1 21 SEQADV 5WN2 GLN A 96 UNP P27695 GLU 96 ENGINEERED MUTATION SEQADV 5WN2 ALA A 138 UNP P27695 CYS 138 ENGINEERED MUTATION SEQADV 5WN2 ASN A 210 UNP P27695 ASP 210 ENGINEERED MUTATION SEQADV 5WN2 GLN B 96 UNP P27695 GLU 96 ENGINEERED MUTATION SEQADV 5WN2 ALA B 138 UNP P27695 CYS 138 ENGINEERED MUTATION SEQADV 5WN2 ASN B 210 UNP P27695 ASP 210 ENGINEERED MUTATION 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 GLN 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 ASN 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 GLN 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 ASN 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 SEQRES 1 C 11 DT DC DG DA DC DG DG DA DT DC DC SEQRES 1 D 9 DG DC DT DG DA DT DG DC DG SEQRES 1 E 21 DG DG DA DT DC DC DG DT DC DG DA DC DC SEQRES 2 E 21 DG DC DA DT DC DA DG DC HET NA A 401 1 HET EDO B 401 4 HET EDO B 402 4 HET EDO B 403 4 HET EDO C 101 4 HET PGA D 101 16 HET CA E 101 1 HET CA E 102 1 HET NA E 103 1 HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PGA 2-PHOSPHOGLYCOLIC ACID HETNAM CA CALCIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 6 NA 2(NA 1+) FORMUL 7 EDO 4(C2 H6 O2) FORMUL 11 PGA C2 H5 O6 P FORMUL 12 CA 2(CA 2+) FORMUL 15 HOH *243(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 SER A 201 1 21 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 SER B 100 LEU B 104 5 5 HELIX 17 AB8 PRO B 105 GLU B 110 5 6 HELIX 18 AB9 ASP B 148 ASP B 152 5 5 HELIX 19 AC1 GLY B 176 VAL B 180 5 5 HELIX 20 AC2 ARG B 181 SER B 201 1 21 HELIX 21 AC3 GLU B 216 LEU B 220 5 5 HELIX 22 AC4 PRO B 223 LYS B 227 5 5 HELIX 23 AC5 THR B 233 VAL B 247 1 15 HELIX 24 AC6 SER B 252 TYR B 257 1 6 HELIX 25 AC7 TYR B 269 ALA B 273 5 5 HELIX 26 AC8 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 SER A 135 N HIS A 116 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 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 ASN A 210 1 O CYS A 208 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 TRP B 67 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 GLU B 161 N LYS B 141 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 ASN 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 APGA D 101 1555 1555 1.55 LINK O3'B DG D 9 P BPGA D 101 1555 1555 1.55 LINK O3' DC E 21 CA CA E 101 1555 1555 2.19 LINK CA CA E 101 O HOH E 209 1555 1555 2.34 LINK CA CA E 101 O HOH B 579 1555 1454 2.31 LINK CA CA E 101 O HOH B 501 1555 1454 2.21 CISPEP 1 VAL A 247 PRO A 248 0 -14.48 CISPEP 2 VAL B 247 PRO B 248 0 -6.67 SITE 1 AC1 2 LYS A 125 TYR A 128 SITE 1 AC2 5 GLN B 137 ALA B 138 LEU B 140 PHE B 162 SITE 2 AC2 5 ASP B 163 SITE 1 AC3 2 GLY B 198 ARG B 202 SITE 1 AC4 4 HIS B 215 GLU B 216 ARG B 237 GLY B 241 SITE 1 AC5 4 MET B 270 DC C 11 DG D 1 DG E 1 SITE 1 AC6 11 GLN A 96 TYR A 171 ASN A 174 ASN A 210 SITE 2 AC6 11 ASN A 212 PHE A 266 LEU A 282 HIS A 309 SITE 3 AC6 11 HOH A 507 DG D 9 HOH D 202 SITE 1 AC7 6 TYR B 171 ASN B 174 HOH B 501 HOH B 579 SITE 2 AC7 6 DC E 21 HOH E 209 SITE 1 AC8 1 ALA B 230 SITE 1 AC9 3 MET B 270 DG E 1 DG E 2 CRYST1 71.363 64.310 91.144 90.00 110.14 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 0.014013 0.000000 0.005140 0.00000 SCALE2 0.000000 0.015550 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011686 0.00000