Aequorin is a Ca-activated bioluminescent protein from jellyfish. This protein contains two sulfhydryl groups, one of which is essential for its bioluminescence. Little information concerning the structure of and relationship between the metal binding sites of aequorin and the sulfhydryl group(s) is known. Aequorin was modified by attachment of either a maleimide spin-label [studied by electron paramagnetic resonance (EPR)] or the fluorescent label Acrylodan at the essential sulfhydryl in order to gain such information. These modifications caused destabilization of the chromophore of aequorin. Both of the attached labels showed considerable freedom of motion. The spin-label was quite accessible to the solvent, and the fluorescent label was less so. In addition the metal binding properties of the spin-labeled aequorin were studied by Mn(II) EPR. One tight Mn(II) binding site per spin-labeled aequorin was found. The distance between the Mn(II) binding site and the spin-label is at least 20 A. Furthermore, the relative affinity of spin-labeled aequorin for various metal ions was found to be in the order Pr(III) greater than Mn(II) greater than Ca(II) greater than Mg(II).