The presence or absence of calcium determines the activation, activity, oligomerization, and stability of blood coagulation factor XIII. To explore these observed effects, we have determined the x-ray crystal structure of recombinant factor XIII A 2 in the presence of calcium, strontium, and ytterbium. The main calcium binding site within each monomer involves the main chain oxygen atom of Ala-457, and also the side chains from residues Asn-436, Asp-438, Glu-485, and Glu-490. Calcium and strontium bind in the same location, while ytterbium binds several angstroms removed. A novel ytterbium binding site is also found at the dimer two-fold axis, near residues Asp-270 and Glu-272, and this site may be related to the reported inhibition by lanthanide metals (Achyuthan, K. E., Mary, A., and Greenberg, C. S. (1989) Biochem. J. 257, 331-338). The overall structure of ion-bound factor XIII is very similar to the previously determined crystal structures of factor XIII zymogen, likely due to the constraints of this monoclinic crystal form. We have merged the three independent sets of water molecules in the structures to determine which water molecules are conserved and possibly structurally significant.The biological importance of factor XIII (fXIII) 1 (EC 2.3.2.13) lies in its ability to form new covalent bonds between protein chains. This activity was first recognized while studying blood coagulation; fXIII was required to form an insoluble clot (1). The activated form of fXIII covalently cross-links two fibrin molecules via an isopeptide bond between the side chains of a glutamine and a lysine located in the C-terminal region of the ␥-chain. Over a longer time period in coagulation, it also forms cross-links between the ␣-and ␥-chains of fibrin (2), and between ␣ 2 -anti-plasmin and fibrin (3). fXIII has been shown to react with more than fibrin (4), and it has recently been found in brain tumors (5) and arthritic joints (6), and there are cases of fXIII deficiencies (7,8). Factor XIII is a member in the family of transglutaminases (TGases), which have a wide range of biological functions (9).Like most coagulation factors, fXIII is synthesized as a zymogen and then cleaved by a protease to become an active enzyme. The structure of fXIII zymogen was determined several years ago (10, 11). In this crystal form, the active site cysteine, Cys-314, is inaccessible to solvent and is not available for catalysis.Physiologically, calcium ions are required for fXIII activation and for TGase activity. In the blood, activation of circulating fXIII requires thrombin cleavage, calcium ions (1.5 mM) (12-14), and fibrin(ogen) (15). High levels of calcium (Ͼ50 mM) can activate fXIII without the use of thrombin (15), and it has recently been shown that platelet fXIII can be activated nonproteolytically in vivo (16).Based on the amino acid sequence, the calcium binding site was predicted to be in a region (residues 468 -479) with high similarity to the EF-hand motif (17, 18). The main calcium binding site, as seen in the preliminary cryst...