1cob

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spinqualitylabelsall models 1cob, resolution 2.0Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

CRYSTAL STRUCTURE SOLUTION AND REFINEMENT OF THE SEMISYNTHETIC COBALT SUBSTITUTED BOVINE ERYTHROCYTE ENZYME SUPEROXIDE DISMUTASE AT 2.0 ANGSTROMS RESOLUTION

Overview

The semisynthetic Co-substituted bovine erythrocyte superoxide dismutase, (SOD) has been crystallized in a new crystalline form and the structure, determined at 2.0 A (1 A = 0.1 nm) resolution. The crystals belong to, space group P2(1)2(1)2(1) with cell constants: a = 51.0, b = 147.6, c =, 47.5 A, and contain one dimeric molecule of 32,000 M(r) per asymmetric, unit. The structure has been solved by molecular replacement techniques, using the Cu,Zn bovine enzyme as a search model, and refined by molecular, dynamics with the crystallographic pseudo-energy term, followed by, conventional crystallographic refinement. The R-factor for the 18,964, unique reflections in the resolution range from 10.0 to 2.0 A is 0.176 for, a model comprising 2188 protein atoms and 200 solvent molecules; the, root-mean-square deviation from the ideal bond lengths is 0.010 A, and the, average atomic temperature factor is 26.5 A2. The dimeric molecule of the, enzyme is composed of two identical subunits related by a, non-crystallographic 2-fold axis. The subunit has as its structural, scaffolding the conventional SOD-flattened antiparallel eight-stranded, beta-barrel, with three external loops. The co-ordination geometry of the, metal center in the active site is fairly well preserved when compared, with the native Cu,Zn bovine enzyme. Co2+ is in tetrahedral co-ordination, while the Cu2+ ligands show an uneven distortion from the square planar, geometry. The least-squares superposition of the metals ligands and the, catalytically important Arg141 of the native and Co-substituted enzyme, yields a root-mean-square value of 0.401 A, the largest deviation, occurring at the Co2+ ligand Asp81. An additional copper ligand, compatible with a water molecule, is observed at 2.38 A from Cu2+ in the, active-site channel, at the supposed binding site of the O2- anion, substrate. Several ordered water molecules have been observed on the, protein surface and in the active-site channel; their structural locations, coincide remarkably with those of related water molecules found in the, crystal structure of the phylogenetically distant superoxide dismutase, from yeast.

About this Structure

1COB is a Single protein structure of sequence from Bos taurus with CU and CO as ligands. Active as Superoxide dismutase, with EC number 1.15.1.1 Full crystallographic information is available from OCA.

Reference

Crystal structure solution and refinement of the semisynthetic cobalt-substituted bovine erythrocyte superoxide dismutase at 2.0 A resolution., Djinovic K, Coda A, Antolini L, Pelosi G, Desideri A, Falconi M, Rotilio G, Bolognesi M, J Mol Biol. 1992 Jul 5;226(1):227-38. PMID:1619651

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