The role of gamma-carboxyglutamic acid in prothrombin has been examined using partially carboxylated variant prothrombins isolated from a person with a hereditary defect in vitamin K-dependent carboxylation. These species differ in gamma-carboxyglutamic acid content, distribution, and function, as monitored by metal binding properties, conformational transitions, phospholipid binding, and calcium-dependent coagulant activity (Borowski, M., Furie, B. C., Goldsmith, G. H., and Furie, B. (1985) J. Biol. Chem. 260, 9258-9264). The distribution of gamma-carboxyglutamic acids in the variant prothrombin species was determined by specific tritium incorporation into gamma-carboxyglutamic acid residues, thermal decarboxylation, and automated Edman degradation. gamma-Carboxyglutamic acid residues in the partially carboxylated prothrombins were identified by the assay of tritium in the resultant glutamic acid residues in the acarboxyprothrombins. The results indicate that variant prothrombins 1-3 are nearly homogeneous populations of partially carboxylated prothrombins. The ability of prothrombin to undergo a metal-induced conformational change and to bind to phospholipid vesicles correlated closely to the presence of a gamma-carboxyglutamic acid at residue 16. This residue is likely involved in the formation of a critical high affinity metal-binding site, possibly formed by Gla 16 and Gla 25 and/or Gla 26. A second high affinity metal-binding site, present in all of the variant prothrombin species, is defined, as an upper limit, by Gla 6, Gla 14, Gla 19, and Gla 20. This region is likely responsible for the interaction of certain of the conformation-specific antibodies to the metal-stabilized conformer of prothrombin.