Refined crystal structure of ytterbium-substituted carp parvalbumin 4.25 at 1.5 A, and its comparison with the native and cadmium-substituted structures.

The crystal structure of carp parvalbumin 4.25 containing a 1:1 molar ratio of ytterbium chloride to protein has been refined at 1.5 A resolution by restrained least-squares methods to a crystallographic R value of 0.199. The crystal structure confirms the NMR studies, which suggest that low concentrations of ytterbium cause an extensive displacement of calcium from the EF metal binding site. A comparison of the ytterbium-substituted model with the native and cadmium-substituted structure show no significant differences, except around the substituted EF metal-binding region. The displacement of calcium by ytterbium at the EF site has caused a movement in the polypeptide backbone of Ser-91 and Asp-92. This movement resulted in an increase in the number of oxygen ligands bound to ytterbium in the EF site from seven to eight.