HEADER HYDROLASE,LYASE/DNA 27-AUG-15 5DG0 TITLE HUMAN APE1 PHOSPHOROTHIOATE SUBSTRATE COMPLEX WITH MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 43-318; COMPND 5 SYNONYM: APEX NUCLEASE,APEN,APURINIC-APYRIMIDINIC ENDONUCLEASE 1,APE- COMPND 6 1,REF-1,REDOX FACTOR-1; COMPND 7 EC: 3.1.-.-,4.2.99.18; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(OMC)P*(48Z) COMPND 11 P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'); COMPND 12 CHAIN: P; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: DNA (5'- COMPND 16 D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 17 3'); COMPND 18 CHAIN: V; COMPND 19 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; 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 KEYWDS HYDROLASE AND LYASE - DNA COMPLEX, HYDROLASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,S.H.WILSON REVDAT 5 27-SEP-23 5DG0 1 HETSYN LINK REVDAT 4 04-DEC-19 5DG0 1 REMARK REVDAT 3 02-DEC-15 5DG0 1 JRNL REVDAT 2 28-OCT-15 5DG0 1 JRNL REVDAT 1 14-OCT-15 5DG0 0 JRNL AUTH B.D.FREUDENTHAL,W.A.BEARD,M.J.CUNEO,N.S.DYRKHEEVA,S.H.WILSON JRNL TITL CAPTURING SNAPSHOTS OF APE1 PROCESSING DNA DAMAGE. JRNL REF NAT.STRUCT.MOL.BIOL. V. 22 924 2015 JRNL REFN ESSN 1545-9985 JRNL PMID 26458045 JRNL DOI 10.1038/NSMB.3105 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 3 NUMBER OF REFLECTIONS : 119514 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.880 REMARK 3 FREE R VALUE TEST SET COUNT : 3441 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 23.9474 - 5.2413 0.98 5310 160 0.1621 0.1520 REMARK 3 2 5.2413 - 4.1673 0.98 5253 156 0.1286 0.1593 REMARK 3 3 4.1673 - 3.6426 0.97 5275 150 0.1381 0.1682 REMARK 3 4 3.6426 - 3.3105 0.97 5199 157 0.1445 0.1870 REMARK 3 5 3.3105 - 3.0738 0.97 5250 154 0.1605 0.2117 REMARK 3 6 3.0738 - 2.8929 0.96 5191 153 0.1777 0.2549 REMARK 3 7 2.8929 - 2.7482 0.93 4973 145 0.1742 0.2299 REMARK 3 8 2.7482 - 2.6287 0.92 4943 149 0.1742 0.2021 REMARK 3 9 2.6287 - 2.5276 0.91 4958 150 0.1715 0.2472 REMARK 3 10 2.5276 - 2.4405 0.90 4880 139 0.1697 0.2504 REMARK 3 11 2.4405 - 2.3643 0.89 4820 150 0.1696 0.2046 REMARK 3 12 2.3643 - 2.2967 0.88 4766 148 0.1711 0.1772 REMARK 3 13 2.2967 - 2.2363 0.88 4748 136 0.1643 0.2500 REMARK 3 14 2.2363 - 2.1818 0.87 4690 135 0.1774 0.2328 REMARK 3 15 2.1818 - 2.1322 0.85 4566 134 0.1687 0.2270 REMARK 3 16 2.1322 - 2.0869 0.83 4462 132 0.1796 0.2041 REMARK 3 17 2.0869 - 2.0452 0.81 4402 140 0.1896 0.2232 REMARK 3 18 2.0452 - 2.0066 0.80 4278 131 0.1950 0.2388 REMARK 3 19 2.0066 - 1.9708 0.78 4249 120 0.2043 0.2444 REMARK 3 20 1.9708 - 1.9374 0.77 4121 114 0.2038 0.2724 REMARK 3 21 1.9374 - 1.9061 0.76 4112 126 0.2033 0.2821 REMARK 3 22 1.9061 - 1.8768 0.74 4081 120 0.2344 0.2130 REMARK 3 23 1.8768 - 1.8492 0.73 3901 110 0.2654 0.2782 REMARK 3 24 1.8492 - 1.8232 0.72 3889 124 0.2759 0.3020 REMARK 3 25 1.8232 - 1.7986 0.69 3756 108 0.2869 0.3040 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.016 5485 REMARK 3 ANGLE : 1.399 7615 REMARK 3 CHIRALITY : 0.051 814 REMARK 3 PLANARITY : 0.006 824 REMARK 3 DIHEDRAL : 19.339 2090 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 5DG0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000213129. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-14 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 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69308 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.799 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4IEM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 20000, 100 MM SODIUM CITRATE, REMARK 280 200 MM MGCL2, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, V 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 SER B 123 REMARK 465 ASP B 124 REMARK 465 LYS B 125 REMARK 465 GLU B 126 REMARK 465 GLY B 127 REMARK 465 GLU B 149 REMARK 465 GLU B 150 REMARK 465 HIS B 151 REMARK 465 ASP B 152 REMARK 465 GLN B 153 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 125 CG CD CE NZ REMARK 470 GLU A 126 CG CD OE1 OE2 REMARK 470 48Z P 11 F2 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 O HOH A 579 O HOH A 621 2.12 REMARK 500 O HOH A 507 O HOH A 509 2.13 REMARK 500 O HOH B 607 O HOH B 656 2.13 REMARK 500 O HOH A 563 O HOH A 677 2.13 REMARK 500 O HOH A 521 O HOH A 696 2.14 REMARK 500 SP3 48Z P 11 O HOH A 504 2.15 REMARK 500 O HOH P 225 O HOH V 133 2.16 REMARK 500 O HOH B 633 O HOH B 641 2.17 REMARK 500 O3' DC V 21 O HOH V 101 2.18 REMARK 500 O HOH A 610 O HOH A 720 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC P 8 O3' DC P 8 C3' -0.043 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 P 15 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DC V 21 O4' - C1' - N1 ANGL. DEV. = 2.1 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 GLU A 110 47.89 -103.92 REMARK 500 LYS A 125 52.31 -146.23 REMARK 500 SER A 129 -152.69 51.51 REMARK 500 ASP A 152 71.14 -105.48 REMARK 500 ARG A 202 -79.49 -110.76 REMARK 500 PHE A 232 26.03 -144.33 REMARK 500 LEU B 111 76.83 -114.77 REMARK 500 SER B 129 -155.20 -151.75 REMARK 500 ARG B 202 -79.45 -114.83 REMARK 500 ASN B 222 68.74 -117.68 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 A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 70 OD1 REMARK 620 2 GLU A 96 OE2 108.0 REMARK 620 3 HOH A 504 O 176.4 75.3 REMARK 620 4 HOH A 516 O 113.9 132.8 63.5 REMARK 620 5 HOH A 527 O 109.1 103.7 68.4 82.5 REMARK 620 N 1 2 3 4 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 ASN B 229 OD1 REMARK 620 2 HOH B 504 O 100.6 REMARK 620 3 HOH B 591 O 166.1 92.4 REMARK 620 4 HOH B 624 O 99.8 70.4 89.1 REMARK 620 5 HOH B 637 O 102.1 103.5 69.8 158.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN P 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 1 N7 REMARK 620 2 HOH P 234 O 100.6 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 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 MN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN P 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN P 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN P 103 DBREF 5DG0 A 43 318 UNP P27695 APEX1_HUMAN 43 318 DBREF 5DG0 B 43 318 UNP P27695 APEX1_HUMAN 43 318 DBREF 5DG0 P 1 21 PDB 5DG0 5DG0 1 21 DBREF 5DG0 V 1 21 PDB 5DG0 5DG0 1 21 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 CYS 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 CYS 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 SEQRES 1 P 21 DG DC DT DG DA DT DG DC DG OMC 48Z DC DG SEQRES 2 P 21 DA DC DG DG DA DT DC DC SEQRES 1 V 21 DG DG DA DT DC DC DG DT DC DG DG DG DC SEQRES 2 V 21 DG DC DA DT DC DA DG DC HET OMC P 10 42 HET 48Z P 11 22 HET MN A 401 1 HET MN A 402 1 HET MN A 403 1 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET CL A 408 1 HET MN B 401 1 HET EDO B 402 4 HET MN P 101 1 HET MN P 102 1 HET MN P 103 1 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM 48Z 2-DEOXY-2-FLUORO-5-O-THIOPHOSPHONO-ALPHA-D- HETNAM 2 48Z ARABINOFURANOSE HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 OMC C10 H16 N3 O8 P FORMUL 3 48Z C5 H10 F O6 P S FORMUL 5 MN 7(MN 2+) FORMUL 8 EDO 5(C2 H6 O2) FORMUL 12 CL CL 1- FORMUL 18 HOH *470(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 GLU A 110 5 6 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 ALA A 273 5 5 HELIX 12 AB3 HIS A 289 PRO A 293 5 5 HELIX 13 AB4 GLY B 71 LYS B 78 1 8 HELIX 14 AB5 LYS B 79 ALA B 88 1 10 HELIX 15 AB6 SER B 100 LEU B 104 5 5 HELIX 16 AB7 PRO B 105 SER B 115 5 11 HELIX 17 AB8 GLY B 176 VAL B 180 5 5 HELIX 18 AB9 ARG B 181 SER B 201 1 21 HELIX 19 AC1 GLU B 216 LEU B 220 5 5 HELIX 20 AC2 PRO B 223 LYS B 227 5 5 HELIX 21 AC3 THR B 233 VAL B 247 1 15 HELIX 22 AC4 SER B 252 TYR B 257 1 6 HELIX 23 AC5 TYR B 269 MET B 271 5 3 HELIX 24 AC6 ASN B 272 ASN B 277 1 6 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 VAL A 131 N SER A 120 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 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 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 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 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 ASP B 210 1 O CYS B 208 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' DG P 9 P AOMC P 10 1555 1555 1.60 LINK O3' DG P 9 P BOMC P 10 1555 1555 1.61 LINK O3'AOMC P 10 P A48Z P 11 1555 1555 1.60 LINK O3'BOMC P 10 P B48Z P 11 1555 1555 1.59 LINK O3 A48Z P 11 P DC P 12 1555 1555 1.60 LINK O3 B48Z P 11 P DC P 12 1555 1555 1.62 LINK OD1 ASP A 70 MN MN A 401 1555 1555 2.16 LINK OE2 GLU A 96 MN MN A 401 1555 1555 2.14 LINK MN MN A 401 O HOH A 504 1555 1555 2.16 LINK MN MN A 401 O HOH A 516 1555 1555 2.28 LINK MN MN A 401 O HOH A 527 1555 1555 2.19 LINK MN MN A 402 O HOH A 604 1555 1555 2.25 LINK OD1 ASN B 229 MN MN B 401 1555 1555 2.18 LINK MN MN B 401 O HOH B 504 1555 1555 1.99 LINK MN MN B 401 O HOH B 591 1555 1555 2.02 LINK MN MN B 401 O HOH B 624 1555 1555 2.20 LINK MN MN B 401 O HOH B 637 1555 1555 2.31 LINK N7 DG P 1 MN MN P 101 1555 1555 2.34 LINK N7 DG P 4 MN MN P 102 1555 1555 2.28 LINK MN MN P 101 O HOH P 234 1555 1555 2.14 LINK MN MN P 103 O HOH P 205 1555 1555 2.20 CISPEP 1 VAL A 247 PRO A 248 0 -4.22 CISPEP 2 VAL B 247 PRO B 248 0 -5.99 SITE 1 AC1 5 ASP A 70 GLU A 96 HOH A 504 HOH A 516 SITE 2 AC1 5 HOH A 527 SITE 1 AC2 2 HOH A 604 HOH A 631 SITE 1 AC3 3 GLY A 225 ASN A 229 DG P 13 SITE 1 AC4 5 ASP A 189 GLY A 239 PHE A 240 HOH A 509 SITE 2 AC4 5 HOH A 539 SITE 1 AC5 7 LEU A 44 TYR A 45 ASN A 277 HOH A 537 SITE 2 AC5 7 HOH A 540 HOH A 613 HOH A 669 SITE 1 AC6 7 LYS A 63 GLU A 86 GLU A 87 LEU A 179 SITE 2 AC6 7 HOH A 510 HOH A 581 HOH A 612 SITE 1 AC7 5 THR A 268 TYR A 269 ASP A 308 DC P 12 SITE 2 AC7 5 DG V 12 SITE 1 AC8 6 GLU A 101 TYR A 118 TRP A 119 HOH A 566 SITE 2 AC8 6 HIS B 116 ARG B 136 SITE 1 AC9 7 LYS B 228 ASN B 229 HOH B 504 HOH B 591 SITE 2 AC9 7 HOH B 624 HOH B 637 DG V 1 SITE 1 AD1 4 ASP B 189 PHE B 240 HOH B 539 HOH B 549 SITE 1 AD2 2 DG P 1 HOH P 234 SITE 1 AD3 1 DG P 4 SITE 1 AD4 2 DG P 16 HOH P 205 CRYST1 44.365 60.601 73.316 83.12 80.68 89.04 P 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 0.022540 -0.000377 -0.003682 0.00000 SCALE2 0.000000 0.016504 -0.001973 0.00000 SCALE3 0.000000 0.000000 0.013921 0.00000