Two stable fluorescent derivatives of molybdopterin have been structurally characterized. Form A is an oxidized pterin with a 6-alkyl substituent. Results of chemical, mass spectral, and NMR studies are consistent with the side chain formulation -C identical to C--CH-OHCH2OPO2-3. Similar studies on the Form B derivative indicate that it is the phosphorylated analog of urothione but lacks the 3-methylthio function. Form B (dephospho) can be synthesized from urothione by desulfuration with Raney nickel and oxidation with SeO2. Chicken liver sulfite oxidase (sulfite:ferricytochrome c oxidoreductase, EC 1.8.2.1) contains one phosphate residue (as molybdopterin) per subunit. The phosphate is noncovalently bound but is not released by trichloroacetic acid at 4 degrees C. The yield of Form A and Form B from sulfite oxidase is 0.50 and 0.27/subunit, respectively. The phosphate ester bond in isolated molybdopterin (Form B) is partially hydrolyzed by 1 N HCl at 100 degrees C (33% in 1 h). The release of inorganic phosphate from sulfite oxidase was more rapid (35% in 10 min) due to the presence of molybdate in the denatured enzyme mixture but slower than expected from a high energy phosphate bond. The presence of molybdopterin in a wide variety of molybdenum- and tungsten-containing enzymes has been demonstrated. Glucose oxidase and the iron and manganese superoxide dismutases are devoid of molybdopterin.