PDB Short entry for 1HD7 HEADER DNA REPAIR 09-NOV-00 1HD7 TITLE A SECOND DIVALENT METAL ION IN THE ACTIVE SITE OF A NEW TITLE 2 CRYSTAL FORM OF HUMAN APURINIC/APYRIDINIMIC ENDONUCLEASE, TITLE 3 APE1, AND ITS IMPLICATIONS FOR THE CATALYTIC MECHANISM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AP ENDONUCLEASE 1, HAP1, REF1, APE1; COMPND 5 EC: 4.2.99.18; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: ALL; SOURCE 6 CELL: ALL; SOURCE 7 ORGANELLE: NUCLEUS; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11D; SOURCE 12 EXPRESSION_SYSTEM_GENE: APE1 KEYWDS DNA REPAIR, ENDONUCLEASE, APE1, HAP1, REF-1 EXPDTA X-RAY DIFFRACTION AUTHOR P.T.BEERNINK,B.W.SEGELKE,B.RUPP REVDAT 5 24-FEB-09 1HD7 1 VERSN REVDAT 4 04-APR-01 1HD7 1 JRNL REVDAT 3 27-MAR-01 1HD7 1 AUTHOR JRNL REVDAT 2 28-FEB-01 1HD7 1 AUTHOR REVDAT 1 16-FEB-01 1HD7 0 JRNL AUTH P.T.BEERNINK,B.W.SEGELKE,M.Z.HADI,J.P.ERZBERGER, JRNL AUTH 2 D.M.WILSON III,B.RUPP JRNL TITL TWO DIVALENT METAL IONS IN THE ACTIVE SITE OF A JRNL TITL 2 NEW CRYSTAL FORM OF HUMAN APURINIC/APYRIMIDINIC JRNL TITL 3 ENDONUCLEASE, APE1: IMPLICATIONS FOR THE CATALYTIC JRNL TITL 4 MECHANISM JRNL REF J.MOL.BIOL. V. 307 1023 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11286553 JRNL DOI 10.1006/JMBI.2001.4529 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.0 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 26771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.0 REMARK 3 FREE R VALUE TEST SET COUNT : 2699 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2070 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 288 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.4 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.13 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.16 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.7 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.016 ; 0.02 REMARK 3 ANGLE DISTANCE (A) : 0.038 ; 0.04 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.069 ; 0.05 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.03 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.15 ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.185 ; 0.3 REMARK 3 MULTIPLE TORSION (A) : 0.261 ; 0.3 REMARK 3 H-BOND (X...Y) (A) : 0.125 ; 0.3 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 0 ; 15 REMARK 3 PLANAR (DEGREES) : 8.4 ; 7 REMARK 3 STAGGERED (DEGREES) : 18.1 ; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 31.7 ; 20 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.8 ; 2 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.7 ; 3 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.2 ; 2 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.4 ; 3 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HD7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-NOV-00. REMARK 100 THE PDBE ID CODE IS EBI-4875. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 4.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL1-5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2398 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : DUAL CRYSTAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34905 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: TO BE PUBLISHED REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.7 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NAOAC PH 4.6, 25% PEG 4K, REMARK 280 1 MM PB(II)OAC, 10-12 MG/ML PROTEIN. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 64.19500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.19500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.42500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 ENDONUCLEOLYTIC CLEAVAGE NEAR APURINIC OR APYRIMIDINIC SITES REMARK 400 TO PRODUCTS WITH 5'-PHOSPHATE. REMARK 400 REPAIRS OXIDATIVE DNA DAMAGES IN VITRO. REMOVES THE BLOCKING REMARK 400 GROUPS FROM THE 3' TERMINI OF THE DNA STRAND BREAKS REMARK 400 GENERATED BY IONIZING RADIATIONS AND BLEOMYCIN. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 GLY A 5 REMARK 465 LYS A 6 REMARK 465 LYS A 7 REMARK 465 GLY A 8 REMARK 465 ALA A 9 REMARK 465 VAL A 10 REMARK 465 ALA A 11 REMARK 465 GLU A 12 REMARK 465 ASP A 13 REMARK 465 GLY A 14 REMARK 465 ASP A 15 REMARK 465 GLU A 16 REMARK 465 LEU A 17 REMARK 465 ARG A 18 REMARK 465 THR A 19 REMARK 465 GLU A 20 REMARK 465 PRO A 21 REMARK 465 GLU A 22 REMARK 465 ALA A 23 REMARK 465 LYS A 24 REMARK 465 LYS A 25 REMARK 465 SER A 26 REMARK 465 LYS A 27 REMARK 465 THR A 28 REMARK 465 ALA A 29 REMARK 465 ALA A 30 REMARK 465 LYS A 31 REMARK 465 LYS A 32 REMARK 465 ASN A 33 REMARK 465 ASP A 34 REMARK 465 LYS A 35 REMARK 465 GLU A 36 REMARK 465 ALA A 37 REMARK 465 ALA A 38 REMARK 465 GLY A 39 REMARK 465 GLU A 40 REMARK 465 GLY A 41 REMARK 465 PRO A 42 REMARK 465 ALA A 43 REMARK 465 ASN A 102 REMARK 465 LYS A 103 REMARK 465 LEU A 104 REMARK 465 PRO A 105 REMARK 465 ALA A 106 REMARK 465 GLU A 107 REMARK 465 LEU A 108 REMARK 465 GLN A 109 REMARK 465 GLU A 110 REMARK 465 LEU A 111 REMARK 465 PRO A 112 REMARK 465 SER A 123 REMARK 465 ASP A 124 REMARK 465 LYS A 125 REMARK 465 GLU A 126 REMARK 465 GLY A 127 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 GLU A 96 OE1 - CD - OE2 ANGL. DEV. = 9.5 DEGREES REMARK 500 CYS A 99 CA - C - O ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG A 136 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 136 NH1 - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 CYS A 138 CA - CB - SG ANGL. DEV. = -8.4 DEGREES REMARK 500 ARG A 177 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 177 NH1 - CZ - NH2 ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 185 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 187 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 187 NH1 - CZ - NH2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 202 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 HIS A 215 CB - CG - ND1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 221 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 221 NH1 - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 GLU A 242 OE1 - CD - OE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 VAL A 247 CA - C - O ANGL. DEV. = -21.8 DEGREES REMARK 500 TYR A 269 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 MET A 270 CA - CB - CG ANGL. DEV. = 12.4 DEGREES REMARK 500 ARG A 274 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 281 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 281 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP A 297 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 301 NE - CZ - NH1 ANGL. DEV. = 3.1 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 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 CYS A 99 -69.40 -142.35 REMARK 500 SER A 100 -142.55 29.14 REMARK 500 GLU A 149 -58.99 -28.79 REMARK 500 MET A 271 19.86 56.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 247 PRO A 248 -70.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CYS A 93 -12.50 REMARK 500 GLN A 117 11.76 REMARK 500 TYR A 118 15.36 REMARK 500 LEU A 179 -18.59 REMARK 500 VAL A 247 -26.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): 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 PB A1319 PB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2282 O REMARK 620 2 GLU A 96 OE1 92.5 REMARK 620 3 GLU A 96 OE2 77.3 45.6 REMARK 620 4 HOH A2069 O 89.2 90.2 47.9 REMARK 620 5 HOH A2079 O 174.9 92.6 106.3 90.7 REMARK 620 6 HOH A2283 O 86.4 175.5 138.1 94.2 88.5 REMARK 620 7 ASP A 70 OD1 85.6 95.4 135.4 172.6 93.9 80.2 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PB A1319 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BIX RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE HUMAN DEOXYRIBONUCLEIC ACID REMARK 900 REPAIR ENDONUCLEASE HAP1 SUGGESTS THE RECOGNITION OF REMARK 900 EXTRA-HELICAL DEOXYRIBOSE AT DEOXYRIBONUCLEIC ACID REMARK 900 ABASIC SITES REMARK 900 RELATED ID: 1CQG RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED REMARK 900 DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, REMARK 900 C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE REMARK 900 COMPRISING ITS TARGET SITE IN HUMAN REF-1 (RESIDUES 59 - REMARK 900 71 OF THE P50 SUBUNIT OF NFKB), NMR, 31 STRUCTURES REMARK 900 RELATED ID: 1CQH RELATED DB: PDB REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED REMARK 900 DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, REMARK 900 C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE REMARK 900 COMPRISING ITS TARGET SITE IN HUMAN REF-1 (RESIDUES 59 - REMARK 900 71 OF THE P50 SUBUNIT OF NFKB), NMR, MINIMIZED AVERAGE REMARK 900 STRUCTURE REMARK 900 RELATED ID: 1DE8 RELATED DB: PDB REMARK 900 HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND REMARK 900 TO ABASIC DEOXYRIBONUCLEIC ACID REMARK 900 RELATED ID: 1DE9 RELATED DB: PDB REMARK 900 HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC REMARK 900 DEOXYRIBONUCLEIC ACID AND MN2+ ION REMARK 900 RELATED ID: 1DEW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC REMARK 900 DEOXYRIBONUCLEIC ACID REMARK 900 RELATED ID: 1E9N RELATED DB: PDB REMARK 900 A SECOND DIVALENT METAL ION IN THE ACTIVE SITE OF A NEW REMARK 900 CRYSTAL FORM OF HUMAN APURINIC/APYRIMIDINIC REMARK 900 ENDONUCLEASE, APE1, AND ITS IMPLICATIONS FOR THE REMARK 900 CATALYTIC MECHANISM DBREF 1HD7 A 1 1 PDB 1HD7 1HD7 1 1 DBREF 1HD7 A 2 318 UNP P27695 APE1_HUMAN 1 317 SEQRES 1 A 318 MET PRO LYS ARG GLY LYS LYS GLY ALA VAL ALA GLU ASP SEQRES 2 A 318 GLY ASP GLU LEU ARG THR GLU PRO GLU ALA LYS LYS SER SEQRES 3 A 318 LYS THR ALA ALA LYS LYS ASN ASP LYS GLU ALA ALA GLY SEQRES 4 A 318 GLU GLY PRO ALA LEU TYR GLU ASP PRO PRO ASP GLN LYS SEQRES 5 A 318 THR SER PRO SER GLY LYS PRO ALA THR LEU LYS ILE CYS SEQRES 6 A 318 SER TRP ASN VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS SEQRES 7 A 318 LYS GLY LEU ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE SEQRES 8 A 318 LEU CYS LEU GLN GLU THR LYS CYS SER GLU ASN LYS LEU SEQRES 9 A 318 PRO ALA GLU LEU GLN GLU LEU PRO GLY LEU SER HIS GLN SEQRES 10 A 318 TYR TRP SER ALA PRO SER ASP LYS GLU GLY TYR SER GLY SEQRES 11 A 318 VAL GLY LEU LEU SER ARG GLN CYS PRO LEU LYS VAL SER SEQRES 12 A 318 TYR GLY ILE GLY ASP GLU GLU HIS ASP GLN GLU GLY ARG SEQRES 13 A 318 VAL ILE VAL ALA GLU PHE ASP SER PHE VAL LEU VAL THR SEQRES 14 A 318 ALA TYR VAL PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU SEQRES 15 A 318 GLU TYR ARG GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE SEQRES 16 A 318 LEU LYS GLY LEU ALA SER ARG LYS PRO LEU VAL LEU CYS SEQRES 17 A 318 GLY ASP LEU ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG SEQRES 18 A 318 ASN PRO LYS GLY ASN LYS LYS ASN ALA GLY PHE THR PRO SEQRES 19 A 318 GLN GLU ARG GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL SEQRES 20 A 318 PRO LEU ALA ASP SER PHE ARG HIS LEU TYR PRO ASN THR SEQRES 21 A 318 PRO TYR ALA TYR THR PHE TRP THR TYR MET MET ASN ALA SEQRES 22 A 318 ARG SER LYS ASN VAL GLY TRP ARG LEU ASP TYR PHE LEU SEQRES 23 A 318 LEU SER HIS SER LEU LEU PRO ALA LEU CYS ASP SER LYS SEQRES 24 A 318 ILE ARG SER LYS ALA LEU GLY SER ASP HIS CYS PRO ILE SEQRES 25 A 318 THR LEU TYR LEU ALA LEU HET PB A1319 1 HETNAM PB LEAD (II) ION FORMUL 2 PB PB 2+ FORMUL 3 HOH *288(H2 O1) HELIX 1 1 GLY A 71 LYS A 78 1 8 HELIX 2 2 LYS A 79 ALA A 88 1 10 HELIX 3 3 ASP A 148 ASP A 152 5 5 HELIX 4 4 GLY A 176 VAL A 180 5 5 HELIX 5 5 ARG A 181 LYS A 203 1 23 HELIX 6 6 GLU A 216 ASP A 219 5 4 HELIX 7 7 ASN A 222 LYS A 227 1 6 HELIX 8 8 THR A 233 VAL A 247 1 15 HELIX 9 9 SER A 252 TYR A 257 1 6 HELIX 10 10 TYR A 269 MET A 271 5 3 HELIX 11 11 ASN A 272 ASN A 277 1 6 HELIX 12 12 HIS A 289 PRO A 293 5 5 SHEET 1 AA 6 HIS A 116 SER A 120 0 SHEET 2 AA 6 VAL A 131 SER A 135 -1 O VAL A 131 N SER A 120 SHEET 3 AA 6 ILE A 91 GLN A 95 -1 O LEU A 92 N LEU A 134 SHEET 4 AA 6 LEU A 62 ASN A 68 1 O CYS A 65 N CYS A 93 SHEET 5 AA 6 ILE A 312 LEU A 316 -1 O ILE A 312 N SER A 66 SHEET 6 AA 6 LEU A 295 ILE A 300 -1 N CYS A 296 O TYR A 315 SHEET 1 AB 6 LYS A 141 TYR A 144 0 SHEET 2 AB 6 VAL A 157 GLU A 161 -1 O VAL A 159 N SER A 143 SHEET 3 AB 6 VAL A 166 TYR A 171 -1 O LEU A 167 N ALA A 160 SHEET 4 AB 6 LEU A 205 ASP A 210 1 O VAL A 206 N VAL A 168 SHEET 5 AB 6 ASP A 283 LEU A 287 -1 O TYR A 284 N GLY A 209 SHEET 6 AB 6 ALA A 250 ASP A 251 -1 O ALA A 250 N LEU A 287 LINK PB PB A1319 O HOH A2282 1555 1555 2.58 LINK PB PB A1319 OE1 GLU A 96 1555 1555 2.56 LINK PB PB A1319 OE2 GLU A 96 1555 1555 3.16 LINK PB PB A1319 O HOH A2069 1555 1555 2.69 LINK PB PB A1319 O HOH A2079 1555 1555 2.76 LINK PB PB A1319 O HOH A2283 1555 1555 2.68 LINK PB PB A1319 OD1 ASP A 70 1555 1555 2.31 SITE 1 AC1 6 ASP A 70 GLU A 96 HOH A2069 HOH A2079 SITE 2 AC1 6 HOH A2282 HOH A2283 CRYST1 128.390 44.850 78.140 90.00 124.54 90.00 C 1 2 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 0.007789 0.000000 0.005361 0.00000 SCALE2 0.000000 0.022296 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015536 0.00000