Manganese and calcium binding sites of concanavalin A

Abstract

The atomic co-ordinates of concanavalin A, a lectin which specifically binds saccharides containing mannosyl and glucosyl residues, have been refined with the fast Fourier least-squares method of Agarwal (1978), with X-ray crystallographic data to 1.75 Å. This metalloprotein contains six co-ordinated Mn2+ and seven co-ordinated Ca2+ which are 4.25 Å apart and are close to the carbohydrate binding site. Both ions are pseudo-octahedral. This is possible for calcium since the average position of two oxygens (from the same carboxyl group) forms one apex of the octahedron. The refinement has improved this region considerably. The ligands for Mn2+ are five oxygens, three from carboxyl side-chains and two from water molecules, and one nitrogen from a histidyl side-chain. The co-ordination sphere for Ca2+ contains seven oxygens, three from two carboxyl side-chains, one from a peptide carbonyl, one from an amide side-chain and, as does Mn2+, two from water molecules. The averages for the five Mn2+O and the seven Ca2+O bonds are 2.28 ± 0.04 (standard deviation) and 2.45 ± 0.09, respectively. For Mn2+, this average is 0.10 Å higher than that found for the Mn(II)hexa-aquoion and is toward the high end of the range usually found for Mn2+O complexes. This is of particular significance since Mn2+ is used as a probe for nuclear magnetic resonance spectroscopic studies of native Mn2+- and Mn2+-substituted metalloproteins. Also, refinement confirms the non-proline cis peptide bond, which is immediately adjacent to the Ca2+ and the carbohydrate binding sites. For the final model, the bond lengths and angles for backbone atoms have root-mean-square deviations from standard values of 0.030 Å and 5.2 deg., and side-chain atoms have slightly lower values. The crystallographic residual, R factor, for this model is 0.167 for 22,042 structure factors. © 1982.