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1e9n

A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism

Method: X-RAY DIFFRACTION Dmax: 92.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE

HOMO SAPIENS

UniProt P27695

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–317 Not recorded PB LEAD (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP, DROP 2+2 UL, 15MG/ML PROTEIN, 1 ML WELL, 0.1M TRIS-HCL, PH 7.5, 0.2M NAOAC, 30% PEG4K, 20MM HECAMEG, 1MM PB(OAC)2, 1MM DTT Resolution 2.20 Å R-free 0.252
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–317 Not recorded PB LEAD (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP, DROP 2+2 UL, 15MG/ML PROTEIN, 1 ML WELL, 0.1M TRIS-HCL, PH 7.5, 0.2M NAOAC, 30% PEG4K, 20MM HECAMEG, 1MM PB(OAC)2, 1MM DTT Resolution 2.20 Å R-free 0.252

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1E9N Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BIX THE CRYSTAL STRUCTURE OF THE HUMAN DNA REPAIR ENDONUCLEASE HAP1 SUGGESTS THE RECOGNITION OF EXTRA-HELICAL DEOXYRIBOSE AT DNA ABASIC SITES Deposited 1998-06-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–317（287 aa）
Not recorded SM SAMARIUM (III) ION × 4 PT PLATINUM (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；pH 7.4
Resolution 2.20 Å R-free 0.269
1CQG HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN REF-1 (RESIDUES 59-71 OF THE P50 SUBUNIT OF NFKB), NMR, 31 STRUCTURES Deposited 1996-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 58–70（13 aa） Fragment：RESIDUES 59 - 71 OF THE P50 SUBUNIT OF NFKB
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1CQH HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN REF-1 (RESIDUES 59-71 OF THE P50 SUBUNIT OF NFKB), NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 58–70（13 aa） Fragment：RESIDUES 59 - 71 OF THE P50 SUBUNIT OF NFKB
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1DE8 HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA Deposited 1999-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 42–317（276 aa） Fragment：APE1
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；MPEG 5000, LITHIUM SULFATE, MES BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.95 Å R-free 0.312
1DE8 HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA Deposited 1999-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 42–317（276 aa） Fragment：APE1
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；MPEG 5000, LITHIUM SULFATE, MES BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.95 Å R-free 0.312
1DE9 HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION Deposited 1999-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 42–317（276 aa） Fragment：APE1
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；MPEG 2000, LITHIUM SULFATE, MANGANESE CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.274
1DE9 HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION Deposited 1999-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 42–317（276 aa） Fragment：APE1
Not recorded MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；MPEG 2000, LITHIUM SULFATE, MANGANESE CHLORIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.274
1DEW CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA Deposited 1999-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 39–317（279 aa） Fragment：APE1
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；MPEG 2000, LITHIUM SULFATE, CACODYLATE BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.65 Å R-free 0.286
1DEW CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA Deposited 1999-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 39–317（279 aa） Fragment：APE1
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；MPEG 2000, LITHIUM SULFATE, CACODYLATE BUFFER, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.65 Å R-free 0.286
1HD7 A Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism Deposited 2000-11-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–317（317 aa）
Not recorded PB LEAD (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；0.1M NAOAC PH 4.6, 25% PEG 4K, 1 MM PB(II)OAC, 10-12 MG/ML PROTEIN.
Resolution 1.95 Å R-free 0.255
2ISI Crystal structure of Ape1 from Homo sapiens in a new crystal form complexed with a ligand Deposited 2006-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–317（317 aa）
Not recorded PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；0.1M hepes, 70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 277K
Resolution 2.76 Å R-free 0.284
2ISI Crystal structure of Ape1 from Homo sapiens in a new crystal form complexed with a ligand Deposited 2006-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–317（317 aa）
Not recorded PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；0.1M hepes, 70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 277K
Resolution 2.76 Å R-free 0.284
2ISI Crystal structure of Ape1 from Homo sapiens in a new crystal form complexed with a ligand Deposited 2006-10-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–317（317 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；0.1M hepes, 70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 277K
Resolution 2.76 Å R-free 0.284
2O3H Crystal structure of the human C65A Ape Deposited 2006-12-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 39–317（279 aa）
Mutation：C65A SM SAMARIUM (III) ION × 2 ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；20% PEG 8000, 100 mM MES pH 6.0, 7.5 mM samarium acetate, 4% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.226
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–318（318 aa）
Not recorded MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K
Resolution 2.15 Å R-free 0.243
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–318（318 aa）
Not recorded MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K
Resolution 2.15 Å R-free 0.243
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–318（318 aa）
Not recorded MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K
Resolution 2.15 Å R-free 0.243
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–318（318 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K
Resolution 2.15 Å R-free 0.243
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–318（318 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K
Resolution 2.15 Å R-free 0.243
3U8U Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form Deposited 2011-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–318（318 aa）
Not recorded MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；280 K；0.05M MGCL2.6H2O, 0.1M HEPES PH 7.5, 30% PEG 550MME, 1 MICRO-MOLAR HYCANTHONE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 280K
Resolution 2.15 Å R-free 0.243
4IEM Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+ Deposited 2012-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 2–318（317 aa）
Not recorded MG MAGNESIUM ION × 3 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；50 mM MES pH 6.0, 200 mM LiSO4, and 25% mPEG 2K, vapor diffusion, hanging drop, temperature 298K
Resolution 2.39 Å R-free 0.246
4IEM Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+ Deposited 2012-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 2–318（317 aa）
Not recorded MG MAGNESIUM ION × 1 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；50 mM MES pH 6.0, 200 mM LiSO4, and 25% mPEG 2K, vapor diffusion, hanging drop, temperature 298K
Resolution 2.39 Å R-free 0.246
4IEM Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+ Deposited 2012-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain C 2–318（317 aa）
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；50 mM MES pH 6.0, 200 mM LiSO4, and 25% mPEG 2K, vapor diffusion, hanging drop, temperature 298K
Resolution 2.39 Å R-free 0.246
4IEM Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+ Deposited 2012-12-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain D 2–318（317 aa）
Not recorded MG MAGNESIUM ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；50 mM MES pH 6.0, 200 mM LiSO4, and 25% mPEG 2K, vapor diffusion, hanging drop, temperature 298K
Resolution 2.39 Å R-free 0.246
4LND Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor Deposited 2013-07-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 39–318（280 aa） Fragment：UNP residues 39-318
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.1 M MES pH 6.5, 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.92 Å R-free 0.241
4LND Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor Deposited 2013-07-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 39–318（280 aa） Fragment：UNP residues 39-318
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.1 M MES pH 6.5, 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.92 Å R-free 0.241
4LND Crystal structure of human apurinic/apyrimidinic endonuclease 1 with essential Mg2+ cofactor Deposited 2013-07-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 39–318（280 aa） Fragment：UNP residues 39-318
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.1 M MES pH 6.5, 30% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 1.92 Å R-free 0.241
4QH9 Crystal structure of Mn2+ bound human APE1 Deposited 2014-05-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 38–318（281 aa） Fragment：UNP residues 38-318
Mutation：C138A EDO 1,2-ETHANEDIOL × 7 MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES, 0.2M Sodium Chloride, 19% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.17 Å R-free 0.256
4QHD Crystal structure of apo human APE1 Deposited 2014-05-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 38–318（281 aa） Fragment：UNP residues 38-318
Mutation：C138A EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES, 0.2M Sodium Chloride, 19% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.65 Å R-free 0.238
4QHE Crystal structure of Mg2+ bound human APE1 Deposited 2014-05-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 38–318（281 aa）
Mutation：C138A MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M MES, 0.2M Sodium Chlorid, 19% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.40 Å R-free 0.193
5CFG C2 crystal form of APE1 with Mg2+ Deposited 2015-07-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–318（275 aa） Fragment：UNP residues 44-318
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20% PEG 8000, 0.2 M MgAc and 0.1 M Cacodylate
Resolution 1.80 Å R-free 0.204
5DFF Human APE1 product complex Deposited 2015-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Not recorded MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Resolution 1.57 Å R-free 0.211
5DFF Human APE1 product complex Deposited 2015-08-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Resolution 1.57 Å R-free 0.211
5DFH Human APE1 mismatch product complex Deposited 2015-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% Peg20000, 100 mM sodium citrate, 200 mM MgCl
Resolution 1.95 Å R-free 0.219
5DFH Human APE1 mismatch product complex Deposited 2015-08-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% Peg20000, 100 mM sodium citrate, 200 mM MgCl
Resolution 1.95 Å R-free 0.219
5DFI Human APE1 phosphorothioate substrate complex Deposited 2015-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 43–318（276 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, 200 mM MgCl
Resolution 1.63 Å R-free 0.195
5DFI Human APE1 phosphorothioate substrate complex Deposited 2015-08-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, 200 mM MgCl
Resolution 1.63 Å R-free 0.195
5DFJ Human APE1 E96Q/D210N mismatch substrate complex Deposited 2015-08-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 43–318（276 aa）
Mutation：E96Q, D210N CL CHLORIDE ION × 6 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, 200 mM MgCl
Resolution 1.85 Å R-free 0.200
5DFJ Human APE1 E96Q/D210N mismatch substrate complex Deposited 2015-08-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：E96Q, D210N CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, 200 mM MgCl
Resolution 1.85 Å R-free 0.200
5DG0 Human APE1 phosphorothioate substrate complex with Mn2+ Deposited 2015-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 43–318（276 aa） Fragment：UNP residues 43-318
Not recorded MN MANGANESE (II) ION × 6 EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% Peg 20000, 100 mM sodium citrate, 200 mM MgCl2
Resolution 1.80 Å R-free 0.205
5DG0 Human APE1 phosphorothioate substrate complex with Mn2+ Deposited 2015-08-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa） Fragment：UNP residues 43-318
Not recorded MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% Peg 20000, 100 mM sodium citrate, 200 mM MgCl2
Resolution 1.80 Å R-free 0.205
5WN0 APE1 exonuclease substrate complex with a C/G match Deposited 2017-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.60 Å R-free 0.275
5WN0 APE1 exonuclease substrate complex with a C/G match Deposited 2017-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.60 Å R-free 0.275
5WN1 APE1 exonuclease product complex Deposited 2017-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Not recorded NA SODIUM ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.30 Å R-free 0.270
5WN1 APE1 exonuclease product complex Deposited 2017-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Not recorded CL CHLORIDE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.30 Å R-free 0.270
5WN2 APE1 exonuclease substrate complex with phosphoglycolate Deposited 2017-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Not recorded NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 PGA 2-PHOSPHOGLYCOLIC ACID × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.29 Å R-free 0.239
5WN2 APE1 exonuclease substrate complex with phosphoglycolate Deposited 2017-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.29 Å R-free 0.239
5WN3 APE1 F266A exonuclease substrate complex with a C/T mismatch Deposited 2017-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Mutation：C138A, F266A CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.00 Å R-free 0.258
5WN3 APE1 F266A exonuclease substrate complex with a C/T mismatch Deposited 2017-07-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–318（276 aa）
Mutation：C138A, F266A EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.00 Å R-free 0.258
5WN4 APE1 exonuclease substrate complex with a C/T mismatch Deposited 2017-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Not recorded NA SODIUM ION × 2 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.10 Å R-free 0.249
5WN4 APE1 exonuclease substrate complex with a C/T mismatch Deposited 2017-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–318（276 aa）
Not recorded NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.10 Å R-free 0.249
5WN5 APE1 exonuclease substrate complex with a C/T mismatch and Mn2+ Deposited 2017-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Not recorded MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.20 Å R-free 0.261
5WN5 APE1 exonuclease substrate complex with a C/T mismatch and Mn2+ Deposited 2017-07-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–318（276 aa）
Not recorded MN MANGANESE (II) ION × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.20 Å R-free 0.261
6BOQ Human APE1 substrate complex with an A/A mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–318（318 aa）
Mutation：C138A EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 1.96 Å R-free 0.258
6BOQ Human APE1 substrate complex with an A/A mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–318（318 aa）
Mutation：C138A EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 1.96 Å R-free 0.258
6BOR Human APE1 substrate complex with an G/G mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–318（318 aa）
Mutation：E96Q, D210N EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 1.84 Å R-free 0.209
6BOR Human APE1 substrate complex with an G/G mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–318（318 aa）
Mutation：E96Q, D210N EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 1.84 Å R-free 0.209
6BOS Human APE1 substrate complex with an A/C mismatch adjacent the THF Deposited 2017-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–318（318 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 2.30 Å R-free 0.236
6BOS Human APE1 substrate complex with an A/C mismatch adjacent the THF Deposited 2017-11-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–318（318 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 2.30 Å R-free 0.236
6BOT Human APE1 substrate complex with an C/C mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–318（318 aa）
Mutation：C138A EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 2.30 Å R-free 0.245
6BOT Human APE1 substrate complex with an C/C mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–318（318 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 2.30 Å R-free 0.245
6BOU Human APE1 substrate complex with an T/C mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–318（318 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 2.54 Å R-free 0.268
6BOU Human APE1 substrate complex with an T/C mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–318（318 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 2.54 Å R-free 0.268
6BOV Human APE1 substrate complex with an A/G mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–318（318 aa）
Mutation：E96Q, D210N, C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 1.98 Å R-free 0.242
6BOV Human APE1 substrate complex with an A/G mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–318（318 aa）
Mutation：E96Q, D210N, C138A PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 1.98 Å R-free 0.242
6BOW Human APE1 substrate complex with an T/T mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–318（318 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 1.59 Å R-free 0.241
6BOW Human APE1 substrate complex with an T/T mismatch adjacent the THF Deposited 2017-11-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–318（318 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2
Resolution 1.59 Å R-free 0.241
6MK3 Crystallographic solvent mapping analysis of DMSO bound to APE1 Deposited 2018-09-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–318（279 aa） Fragment：UNP residues 40-318
Not recorded DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6.0, 200 mM sodium chloride, 18-21% PEG4000
Resolution 1.48 Å R-free 0.219
6MKK Crystallographic solvent mapping analysis of DMSO/Mg bound to APE1 Deposited 2018-09-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–318（279 aa） Fragment：UNP residues 40-318
Not recorded MG MAGNESIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6.0, 200 mM sodium chloride, 18-21% PEG4000
Resolution 1.44 Å R-free 0.212
6MKM Crystallographic solvent mapping analysis of DMSO/Tris bound to APE1 Deposited 2018-09-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–318（279 aa） Fragment：UNP residues 40-318
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6.0, 200 mM sodium chloride, 18-21% PEG4000
Resolution 1.67 Å R-free 0.250
6MKO Crystallographic solvent mapping analysis of glycerol bound to APE1 Deposited 2018-09-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 40–318（279 aa） Fragment：UNP residues 40-318
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM MES, pH 6.0, 200 mM sodium chloride, 18-21% PEG4000
Resolution 2.09 Å R-free 0.228
6P93 Human APE1 K98A AP-endonuclease product complex Deposited 2019-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: pentameric
Chain A 43–318（276 aa）
Chain B 43–318（276 aa）
Mutation：K98A Mutation：K98A MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Resolution 2.10 Å R-free 0.226
6P94 Human APE1 C65A AP-endonuclease product complex Deposited 2019-06-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: pentameric
Chain A 43–318（276 aa）
Chain B 43–318（276 aa）
Not recorded MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Resolution 2.09 Å R-free 0.244
6W0Q APE1 endonuclease product complex D148E Deposited 2020-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Mutation：D148E MG MAGNESIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Resolution 1.89 Å R-free 0.223
6W0Q APE1 endonuclease product complex D148E Deposited 2020-03-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：D148E EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Resolution 1.89 Å R-free 0.223
6W2P APE1 endonuclease product complex L104R Deposited 2020-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Mutation：L104R MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Resolution 1.94 Å R-free 0.238
6W2P APE1 endonuclease product complex L104R Deposited 2020-03-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：L104R EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Resolution 1.94 Å R-free 0.238
6W3L APE1 exonuclease substrate complex wild-type Deposited 2020-03-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Not recorded CA CALCIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.59 Å R-free 0.277
6W3L APE1 exonuclease substrate complex wild-type Deposited 2020-03-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–318（276 aa）
Not recorded NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.59 Å R-free 0.277
6W3N APE1 exonuclease substrate complex D148E Deposited 2020-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Mutation：D148E CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.69 Å R-free 0.308
6W3N APE1 exonuclease substrate complex D148E Deposited 2020-03-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–318（276 aa）
Mutation：D148E EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.69 Å R-free 0.308
6W3Q APE1 exonuclease substrate complex L104R Deposited 2020-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Mutation：L104R NA SODIUM ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.49 Å R-free 0.259
6W3Q APE1 exonuclease substrate complex L104R Deposited 2020-03-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–318（276 aa）
Mutation：L104R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.49 Å R-free 0.259
6W3U APE1 exonuclease substrate complex R237C Deposited 2020-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Mutation：R237C CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.40 Å R-free 0.250
6W3U APE1 exonuclease substrate complex R237C Deposited 2020-03-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–318（276 aa）
Mutation：R237C EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.40 Å R-free 0.250
6W43 APE1 AP-endonuclease product complex R237C Deposited 2020-03-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Mutation：R237C EDO 1,2-ETHANEDIOL × 2 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Resolution 1.99 Å R-free 0.224
6W43 APE1 AP-endonuclease product complex R237C Deposited 2020-03-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：R237C EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Resolution 1.99 Å R-free 0.224
6W4I APE1 Y269A product complex with abasic DNA Deposited 2020-03-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Mutation：Y269A, C138A MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；24% PEG 3350, 0.1 M Bis Tris Propane (pH 6.5), 0.2 M Sodium Fluoride
Resolution 2.20 Å R-free 0.227
6W4I APE1 Y269A product complex with abasic DNA Deposited 2020-03-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Mutation：Y269A, C138A MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；24% PEG 3350, 0.1 M Bis Tris Propane (pH 6.5), 0.2 M Sodium Fluoride
Resolution 2.20 Å R-free 0.227
6W4T APE1 Y269A phosphorothioate substrate complex with abasic DNA Deposited 2020-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 43–318（276 aa）
Mutation：Y269A, C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；27% PEG 3350, 100 mM Bis Tris Propane (pH 6.5), 200 mM Sodium Fluoride
Resolution 2.77 Å R-free 0.274
6W4T APE1 Y269A phosphorothioate substrate complex with abasic DNA Deposited 2020-03-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 43–318（276 aa）
Mutation：Y269A, C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；27% PEG 3350, 100 mM Bis Tris Propane (pH 6.5), 200 mM Sodium Fluoride
Resolution 2.77 Å R-free 0.274
7LPG APE1 product complex with abasic ribonucleotide DNA Deposited 2021-02-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；200 mM MgCl2, 100 mM Sodium Citrate (pH 5), 10-15% PEG 20,000
Resolution 2.08 Å R-free 0.263
7LPG APE1 product complex with abasic ribonucleotide DNA Deposited 2021-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain D 43–318（276 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；200 mM MgCl2, 100 mM Sodium Citrate (pH 5), 10-15% PEG 20,000
Resolution 2.08 Å R-free 0.263
7LPH APE1 Mn-bound product complex with abasic ribonucleotide DNA Deposited 2021-02-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200 mM MgCl2, 100 mM Sodium Citrate (pH 5), 10-15% PEG 20,000
Resolution 1.99 Å R-free 0.237
7LPH APE1 Mn-bound product complex with abasic ribonucleotide DNA Deposited 2021-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain D 43–318（276 aa）
Mutation：C138A MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200 mM MgCl2, 100 mM Sodium Citrate (pH 5), 10-15% PEG 20,000
Resolution 1.99 Å R-free 0.237
7LPI APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA Deposited 2021-02-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；50 mM tri-Sodium Citrate (pH 4), 100 mM NaCl, 10% Peg 6,000
Resolution 2.05 Å R-free 0.245
7LPI APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA Deposited 2021-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 43–318（276 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；50 mM tri-Sodium Citrate (pH 4), 100 mM NaCl, 10% Peg 6,000
Resolution 2.05 Å R-free 0.245
7LPJ APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA Deposited 2021-02-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；50 mM tri-Sodium Citrate (pH 4), 100 mM NaCl, 10% Peg 6,000
Resolution 2.56 Å R-free 0.248
7LPJ APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA Deposited 2021-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain D 43–318（276 aa）
Mutation：C138A MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；291 K；50 mM tri-Sodium Citrate (pH 4), 100 mM NaCl, 10% Peg 6,000
Resolution 2.56 Å R-free 0.248
7MCR Human Apex/Ref1 homodimer formed under oxidative condition Deposited 2021-04-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 44–318（275 aa）
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293.15 K；100 mM MES/ sodium hydroxide, 200 mM calcium acetate, 20% W/V PEG 8000
Resolution 1.90 Å R-free 0.233
7MEV Human Apex/Ref1 monomer with C138A mutation Deposited 2021-04-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–318（275 aa）
Mutation：C138A MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277.15 K；20 %w/v PEG 3350, 200 mM Sodium nitrate
Resolution 1.60 Å R-free 0.196
7SUV APE1 exonuclease substrate complex with 8oxoG opposite A Deposited 2021-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Mutation：E96Q, C138A, D210N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 1.99 Å R-free 0.265
7SUV APE1 exonuclease substrate complex with 8oxoG opposite A Deposited 2021-11-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–318（276 aa）
Mutation：E96Q, C138A, D210N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 1.99 Å R-free 0.265
7SVB APE1 exonuclease substrate complex with 8oxoG opposite C Deposited 2021-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Mutation：E96Q, C138A, D210N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.24 Å R-free 0.245
7SVB APE1 exonuclease substrate complex with 8oxoG opposite C Deposited 2021-11-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–318（276 aa）
Mutation：E96Q, C138A, D210N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；7 - 14% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Resolution 2.24 Å R-free 0.245
7TC2 Human APE1 in complex with 5-nitroindole-2-carboxylic acid Deposited 2021-12-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 39–318（280 aa）
Not recorded GID 5-nitro-1H-indole-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG3350, Sodium Formate
Resolution 1.43 Å R-free 0.270
7TC2 Human APE1 in complex with 5-nitroindole-2-carboxylic acid Deposited 2021-12-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 39–318（280 aa）
Not recorded GID 5-nitro-1H-indole-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG3350, Sodium Formate
Resolution 1.43 Å R-free 0.270
7TC2 Human APE1 in complex with 5-nitroindole-2-carboxylic acid Deposited 2021-12-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 39–318（280 aa）
Not recorded GID 5-nitro-1H-indole-2-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG3350, Sodium Formate
Resolution 1.43 Å R-free 0.270
7TC2 Human APE1 in complex with 5-nitroindole-2-carboxylic acid Deposited 2021-12-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 39–318（280 aa）
Not recorded GID 5-nitro-1H-indole-2-carboxylic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG3350, Sodium Formate
Resolution 1.43 Å R-free 0.270
7TC3 Human APE1 in the apo form Deposited 2021-12-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 39–318（280 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；PEG3350, Sodium Formate
Resolution 1.25 Å R-free 0.178
7TR7 APE1 product complex with abasic ssDNA Deposited 2022-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 43–318（276 aa）
Mutation：C138A MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.05M KCl, 0.05M sodium cacodylate pH 6, 10% PEG 8,000, 5mM spermine, 5mM L-Argininamide dihydrochloride
Resolution 2.00 Å R-free 0.215
7TR7 APE1 product complex with abasic ssDNA Deposited 2022-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 43–318（276 aa）
Mutation：C138A MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.05M KCl, 0.05M sodium cacodylate pH 6, 10% PEG 8,000, 5mM spermine, 5mM L-Argininamide dihydrochloride
Resolution 2.00 Å R-free 0.215
7U50 APE1 bound to a nucleosome core particle with AP-site at SHL-6 Deposited 2022-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric
Chain K 1–318（318 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9DP1 APE1 N174A Substrate Complex with Abasic DNA Deposited 2024-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 43–318（276 aa）
Mutation：tr1-42, C138A, N174A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM sodium citrate, pH 5.0, 200 mM magnesium chloride, 16-21% PEG20000
Resolution 2.29 Å R-free 0.251
9DP1 APE1 N174A Substrate Complex with Abasic DNA Deposited 2024-09-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：tr1-42, C138A, N174A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM sodium citrate, pH 5.0, 200 mM magnesium chloride, 16-21% PEG20000
Resolution 2.29 Å R-free 0.251
9DP2 APE1 N174A Product Complex with Abasic DNA Deposited 2024-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Mutation：tr1-42, C138A, N174A MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM sodium citrate, pH 5.0, 200 mM magnesium chloride, 16-21% PEG20000
Resolution 1.99 Å R-free 0.203
9DP2 APE1 N174A Product Complex with Abasic DNA Deposited 2024-09-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：tr1-42, C138A, N174A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM sodium citrate, pH 5.0, 200 mM magnesium chloride, 16-21% PEG20000
Resolution 1.99 Å R-free 0.203
9DP3 APE1 N174D Product Complex with Abasic DNA Deposited 2024-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Mutation：tr1-42, C138A, N174D SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM lithium sulfate, 15-25% PEG3350
Resolution 2.10 Å R-free 0.274
9DP3 APE1 N174D Product Complex with Abasic DNA Deposited 2024-09-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 43–318（276 aa）
Mutation：tr1-42, C138A, N174D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；200 mM lithium sulfate, 15-25% PEG3350
Resolution 2.10 Å R-free 0.274
9DP4 APE1 N174Q Product Complex with Abasic DNA Deposited 2024-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 43–318（276 aa）
Mutation：tr1-42, C138A, N174Q PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM HEPES free acid, 200 mM ammonium acetate, 25% PEG3350
Resolution 2.25 Å R-free 0.248
9DP4 APE1 N174Q Product Complex with Abasic DNA Deposited 2024-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 43–318（276 aa）
Mutation：tr1-42, C138A, N174Q PEG DI(HYDROXYETHYL)ETHER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM HEPES free acid, 200 mM ammonium acetate, 25% PEG3350
Resolution 2.25 Å R-free 0.248
9RQS Human APE1 in complex with DNA Deposited 2025-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 39–318（280 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M ammonium sulfate, 0.1 M Na HEPES pH 7, 20% w/v PEG 4000
Resolution 1.70 Å R-free 0.228

66 other PDB entries and 122 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name APE1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–318； UniProt 1–317 Author chain B； PDBConstruct 2–318； UniProt 1–317

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1e9n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1e9n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1e9n
Deposition date deposition_date2000-10-24
Structure title titleA second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism
Keywords keywordsDNA REPAIR, DNA REPAIR ENDONUCLEASE, BASE EXCISION REPAIR, ABASIC ENDONUCLEASE, APE1, HAP1, REF-1, ALPHA, BETA SANDWICH; DNA REPAIR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.46 Å
Radius of gyration Rg (electron density) rg_electron27.95 Å
Forward intensity I(0) i064766900.00
Molecular weight molecular_weight62257.0 kDa
Excluded volume excluded_volume77298 ų
Envelope volume envelope_volume93101 ų
Hydration-shell volume shell_volume28711 ų
Envelope diameter envelope_diameter101.4 Å
Shell Rg shell_rg34.15 Å
Envelope Rg envelope_rg27.94 Å
Shape Rg shape_rg27.94 Å
Total Rg total_rg28.58 Å
Total atoms total_atoms4340
Residues n_residues548
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.4 Å
Rg (real space) rg_real28.64 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real6.4770e+07
I(0) uncertainty (real space) i0_real_error1.0220e+06
Rg (reciprocal space) rg_reciprocal28.59 Å
I(0) (reciprocal space) i0_reciprocal64760000.0000
Solution quality estimate total_estimate0.7812
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.4 Å
Skewness Skewness skewness0.412
Kurtosis Kurtosis kurtosis-0.605
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22900000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.770; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.849; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1e9na_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.151 — DNase I-like
Superfamily Superfamily superfamilyd.151.1 — DNase I-like
Family Family familyd.151.1.1 — DNase I-like
Domain ID domain_idd1e9nb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.151 — DNase I-like
Superfamily Superfamily superfamilyd.151.1 — DNase I-like
Family Family familyd.151.1.1 — DNase I-like

CATH v4.4 (2 domains)

Domain ID domain_id1e9nA00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily10 — Endonuclease/exonuclease/phosphatase
Domain ID domain_id1e9nB00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily10 — Endonuclease/exonuclease/phosphatase
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8. Citations (1)

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9. Files and Curves (10)