2sod

DETERMINATION AND ANALYSIS OF THE 2 ANGSTROM STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE

Method: X-RAY DIFFRACTION D_max: 82.0 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

COPPER,ZINC SUPEROXIDE DISMUTASE

Bos taurus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain O； UniProt 1–151 Chain Y； UniProt 1–151	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 Å
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–151 Chain G； UniProt 1–151	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 Å

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 2SOD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CB4 CRYSTAL STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE Deposited 1999-02-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；277 K；pH 6.00, temperature 277.00K	Resolution 2.30 Å R-free 0.228
1CBJ CRYSTAL STRUCTURE OF BOVINE SUPEROXIDE DISMUTASE CRYSTAL. Deposited 1999-02-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 1.65 Å R-free 0.228
1COB CRYSTAL STRUCTURE SOLUTION AND REFINEMENT OF THE SEMISYNTHETIC COBALT SUBSTITUTED BOVINE ERYTHROCYTE ENZYME SUPEROXIDE DISMUTASE AT 2.0 ANGSTROMS RESOLUTION Deposited 1992-02-19	Different mutation/modification Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 CO COBALT (II) ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1E9O Crystal structure of bovine SOD - 1 of 3 Deposited 2000-10-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；PEG-4000, NACL, pH 4.00	Resolution 1.85 Å R-free 0.230
1E9P Crystal structure of bovine Cu, Zn SOD to 1.7 Angstrom (3 of 3) Deposited 2000-10-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 1.70 Å R-free 0.202
1E9Q Crystal structure of bovine Cu Zn SOD - (1 of 3) Deposited 2000-10-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 3 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 1.75 Å R-free 0.205
1Q0E Atomic resolution (1.15 ) crystal structure of bovine copper, zinc superoxide dismutase Deposited 2003-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–151（151 aa） Fragment：Copper, Zinc Superoxide Dismutase	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15 % PEG-4000, 50 mM glycyl-glycine , 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.15 Å R-free 0.166
1Q0E Atomic resolution (1.15 ) crystal structure of bovine copper, zinc superoxide dismutase Deposited 2003-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–151（151 aa） Fragment：Copper, Zinc Superoxide Dismutase	Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15 % PEG-4000, 50 mM glycyl-glycine , 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.15 Å R-free 0.166
1SDA CRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXIDE DISMUTASE Deposited 1993-01-13	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–151（151 aa） Chain Y 1–151（151 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1SDA CRYSTAL STRUCTURE OF PEROXYNITRITE-MODIFIED BOVINE CU,ZN SUPEROXIDE DISMUTASE Deposited 1993-01-13	Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–151（151 aa） Chain G 1–151（151 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1SXA CRYSTAL STRUCTURE OF REDUCED BOVINE ERYTHROCYTE SUPEROXIDE DISMUTASE AT 1.9 ANGSTROMS RESOLUTION Deposited 1995-03-17	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1SXB CRYSTAL STRUCTURE OF REDUCED BOVINE ERYTHROCYTE SUPEROXIDE DISMUTASE AT 1.9 ANGSTROMS RESOLUTION Deposited 1995-03-17	Different mutation/modification	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1SXC CRYSTAL STRUCTURE OF REDUCED BOVINE ERYTHROCYTE SUPEROXIDE DISMUTASE AT 1.9 ANGSTROMS RESOLUTION Deposited 1995-03-17	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1SXN REDUCED BOVINE SUPEROXIDE DISMUTASE AT PH 5.0 Deposited 1997-09-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions excess nitrogen atmosphere；pH 5；20 % PEG6K, 20MM HEPES PH 5.0, SODIUM DITHIONITE (EXCESS), NITROGEN ATMOSPHERE, excess nitrogen atmosphere	Resolution 1.90 Å
1SXS Reduced bovine superoxide dismutase at pH 5.0 complexed with thiocyanate Deposited 1998-09-24	Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	SCN THIOCYANATE ION × 2 CU COPPER (II) ION × 2 ZN ZINC ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions excess nitrogen atmosphere；pH 5；20 % PEG6K, 20MM HEPES, 100MM NASCN, PH 5.0, SODIUM DITHIONITE (EXCESS), NITROGEN ATMOSPHERE, excess nitrogen atmosphere	Resolution 2.00 Å
1SXZ Reduced bovine superoxide dismutase at pH 5.0 complexed with azide Deposited 1998-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 CA CALCIUM ION × 2 AZI AZIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions excess nitrogen atmosphere；pH 5；20 % PEG6K, 20MM HEPES PH 5.0, SODIUM DITHIONITE (EXCESS), NITROGEN ATMOSPHERE, excess nitrogen atmosphere	Resolution 2.05 Å
2AEO Crystal structure of cisplatinated bovine Cu,Zn superoxide dismutase Deposited 2005-07-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–151（151 aa） Chain B 1–151（151 aa）	Not recorded	CU COPPER (II) ION × 4 ZN ZINC ION × 4 CPT Cisplatin × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；50mM Tris HCl, 18% PEG 4000, 20% 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.236
2Z7U Crystal Structure of H2O2 treated Cu,Zn-SOD Deposited 2007-08-28	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4-6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.10 Å R-free 0.238
2Z7W Crystal Structure of H2O2 treated Cu,Zn-SOD Deposited 2007-08-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4-6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.234
2Z7Y Crystal Structure of H2O2 treated Cu,Zn-SOD Deposited 2007-08-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4-6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.55 Å R-free 0.210
2Z7Z Crystal Structure of H2O2 treated Cu,Zn-SOD Deposited 2007-08-30	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	ZN ZINC ION × 2 CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4-6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.85 Å R-free 0.228
2ZOW Crystal Structure of H2O2 treated Cu,Zn-SOD Deposited 2008-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	ZN ZINC ION × 2 CU1 COPPER (I) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；295 K；20% (w/v) PEG 4000, 20% (w/v) iso-propanol, 0.09M MES, 1mM EDTA, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.45 Å R-free 0.221
3HW7 High pressure (0.57 GPa) crystal structure of bovine copper, zinc superoxide dismutase at 2.0 angstroms Deposited 2009-06-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	CU1 COPPER (I) ION × 2 ZN ZINC ION × 2 CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.218
3SOD CHANGES IN CRYSTALLOGRAPHIC STRUCTURE AND THERMOSTABILITY OF A CU,ZN SUPEROXIDE DISMUTASE MUTANT RESULTING FROM THE REMOVAL OF BURIED CYSTEINE Deposited 1990-06-26	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–151（151 aa） Chain Y 1–151（151 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
3SOD CHANGES IN CRYSTALLOGRAPHIC STRUCTURE AND THERMOSTABILITY OF A CU,ZN SUPEROXIDE DISMUTASE MUTANT RESULTING FROM THE REMOVAL OF BURIED CYSTEINE Deposited 1990-06-26	Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–151（151 aa） Chain G 1–151（151 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–152（151 aa） Chain D 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 2–152（151 aa） Chain F 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 2–152（151 aa） Chain H 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 2–152（151 aa） Chain J 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 2–152（151 aa） Chain L 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain M 2–152（151 aa） Chain N 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 H2S HYDROSULFURIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
8IQ0 Crystal structure of hydrogen sulfide-bound superoxide dismutase in oxidized state Deposited 2023-03-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 2–152（151 aa） Chain P 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25%PEG4000, 150mM ammonium sulfate and 100 mM MES	Resolution 1.88 Å R-free 0.244
8IQ1 Crystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state Deposited 2023-03-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–152（151 aa） Chain B 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 5 H2S HYDROSULFURIC ACID × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 4000, 150 mM amimonium sulfate and 100 mM MES, pH 5.5	Resolution 1.80 Å R-free 0.217
8IQ1 Crystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state Deposited 2023-03-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–152（151 aa） Chain D 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 4000, 150 mM amimonium sulfate and 100 mM MES, pH 5.5	Resolution 1.80 Å R-free 0.217
8IQ1 Crystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state Deposited 2023-03-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 2–152（151 aa） Chain F 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 H2S HYDROSULFURIC ACID × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 4000, 150 mM amimonium sulfate and 100 mM MES, pH 5.5	Resolution 1.80 Å R-free 0.217
8IQ1 Crystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state Deposited 2023-03-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 2–152（151 aa） Chain H 2–152（151 aa）	Not recorded	CU COPPER (II) ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 5 H2S HYDROSULFURIC ACID × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 4000, 150 mM amimonium sulfate and 100 mM MES, pH 5.5	Resolution 1.80 Å R-free 0.217

24 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SODC_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 2–152； UniProt 1–151 Author chain G； PDBConstruct 2–152； UniProt 1–151 Author chain O； PDBConstruct 2–152； UniProt 1–151 Author chain Y； PDBConstruct 2–152； UniProt 1–151

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2sod
Deposition date deposition_date	1980-03-25
Structure title title	DETERMINATION AND ANALYSIS OF THE 2 ANGSTROM STRUCTURE OF COPPER, ZINC SUPEROXIDE DISMUTASE
Keywords keywords	OXIDOREDUCTASE (SUPEROXIDE ACCEPTOR); OXIDOREDUCTASE (SUPEROXIDE ACCEPTOR)
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.84 Å
Radius of gyration Rg (electron density) rg_electron	27.00 Å
Forward intensity I(0) i0	73594600.00
Molecular weight molecular_weight	62873.0 kDa
Excluded volume excluded_volume	76952 Å³
Envelope volume envelope_volume	97037 Å³
Hydration-shell volume shell_volume	30056 Å³
Envelope diameter envelope_diameter	88.1 Å
Shell Rg shell_rg	34.34 Å
Envelope Rg envelope_rg	26.71 Å
Shape Rg shape_rg	27.02 Å
Total Rg total_rg	27.66 Å
Total atoms total_atoms	4388
Residues n_residues	604
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	82.0 Å
Rg (real space) rg_real	27.69 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	7.3590e+07
I(0) uncertainty (real space) i0_real_error	9.6780e+05
Rg (reciprocal space) rg_reciprocal	27.74 Å
I(0) (reciprocal space) i0_reciprocal	73600000.0000
Solution quality estimate total_estimate	0.9136
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	80.6 Å
Skewness Skewness skewness	0.061
Kurtosis Kurtosis kurtosis	-0.699
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8351000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.984; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.922

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	COPPER,ZINC SUPEROXIDE DISMUTASE
Molecular weight formula_weight	15599.4 kDa
EC 编号 ec_number	1.15.1.1
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,Y,B,G
Atom count atom_count	4392

XATKAVCVLKGDGPVQGTIHFEAKGDTVVVTGSITGLTEGDHGFHVHQFGDNTQGCTSAGPHFNPLSKKHGGPKDEERHVGDLGNVTADKNGVAIVDIVDPLISLSGEYSIIGRTMVVHEKPDDLGRGGNEESTKTGNAGSRLACGVIGIAK

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2sodb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d2sodg_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d2sodo_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d2sody_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

CATH v4.4 (4 domains)

Domain ID domain_id	2sodB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	2sodG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	2sodO00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	2sodY00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

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8. Citations (9)

Determination and analysis of the 2 A-structure of copper, zinc superoxide dismutase.

J.Mol.Biol. (1982)

PMID: 7175933 · DOI: 10.1016/0022-2836(82)90174-7 PRIMARY

Structure and Mechanism of Copper, Zinc Superoxide Dismutase

Nature (1983)

Electrostatic Recognition between Superoxide and Copper, Zinc Superoxide Dismutase

Nature (1983)

Metal Sites of Copper-Zinc Superoxide Dismutase

Biochemistry (1977)

Similarity of Three-Dimensional Structure between the Immunoglobulin Domain and the Copper,Zinc Superoxide Dismutase Subunit

J.Mol.Biol. (1976)

Alpha-Carbon Coordinates for Bovine Cu,Zn Superoxide Dismutase

Biochem.Biophys.Res.Commun. (1975)

Crystal Structure of Bovine Cu,Zn Superoxide Dismutase at 3 Angstroms Resolution,Chain Tracing and Metal Ligands

Proc.Natl.Acad.Sci.USA (1975)

The Crystal Structure of Bovine Cu2+,Zn2+ Superoxide Dismutase at 5.5 Angstroms Resolution

J.Biol.Chem. (1974)

Two Crystal Forms of Bovine Superoxide Dismutase

J.Biol.Chem. (1972)

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Unit-cell length a length_a	93.650 Å
Unit-cell length b length_b	90.330 Å
Unit-cell length c length_c	71.650 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	0.2560
R_free r_free	—

fit	/app/data/saxs_computation/so/2sod/2sod.fit
pddf	/app/data/pr_computation/so/2sod/2sod.pr.out
profile	/app/data/saxs_computation/so/2sod/2sod.dat