1SRD

Three-dimensional structure of CU,ZN-superoxide dismutase from spinach at 2.0 Angstroms resolution

Summary for 1SRD

• Entry DOI: 10.2210/pdb1srd/pdb
• Descriptor: COPPER,ZINC SUPEROXIDE DISMUTASE, COPPER (II) ION, ZINC ION, ... (4 entities in total)
• Functional Keywords: superoxide acceptor, oxidoreductase
• Biological source: Spinacia oleracea (spinach)
• Cellular location: Plastid, chloroplast: P07505
• Total number of polymer chains: 4
• Total formula weight: 63389.43

Authors

Kitagawa, Y.,Katsube, Y. (deposition date: 1993-04-15, release date: 1994-01-31, Last modification date: 2024-11-20)

Primary citation

Kitagawa, Y.,Tanaka, N.,Hata, Y.,Kusunoki, M.,Lee, G.P.,Katsube, Y.,Asada, K.,Aibara, S.,Morita, Y.
Three-dimensional structure of Cu,Zn-superoxide dismutase from spinach at 2.0 A resolution.
J.Biochem.(Tokyo), 109:477-485, 1991

PubMed Abstract: The three-dimensional structure of Cu,Zn-superoxide dismutase from spinach leaves has been determined by X-ray crystal structure analysis. The atomic coordinates were refined at 2.0 A resolution using the Hendrickson and Konnert program for stereochemically restrained refinement against structure factors, which allowed the use of non-crystallographic symmetry. The crystallographic residual error for the refined model was 24.9%, with a root mean square deviation of 0.03 A from the ideal bond length and an average atomic temperature factor of 9.6 A. A dimeric molecule of the enzyme is comprised of two identical subunits related by a non-crystallographic 2-fold axis. Each subunit of 154 amino acid residues is composed primarily of eight anti-parallel beta-strands that form a flattened cylinder, plus three external loops. The main-chain hydrogen bonds primarily link the beta-strands. The overall structure of this enzyme is quite similar to that of the bovine dismutase except for some parts. The single disulfide bridge (Cys57-Cys146) and the salt bridge (Arg79-Asp101) may stabilize the loop regions of the structure. The Cu2+ and Zn2+ ions in the active site lie 6.1 A apart at the bottom of the long channel. The Cu2+ ligands (ND1 of His-46, and NE2 of His-48, -63, and -120) show an uneven tetrahedral distortion from a square plane. The Zn2+ ligands (ND1 of His-63, -71, and -80 and OD1 of Asp-83) show an almost tetrahedral geometry. The imidazole ring of His-63 forms a bridge between the Cu2+ and Zn2+ ions.(ABSTRACT TRUNCATED AT 250 WORDS)

PubMed: 1880134

Experimental method

X-RAY DIFFRACTION (2 Å)