The limitations of X-ray absorption spectroscopy for determining the structure of zinc sites in proteins. When is a tetrathiolate not a tetrathiolate?

X-ray absorption fine structure (XAFS) spectra have been measured for a series of structurally characterized zinc model complexes that mimic the zinc sites found in metalloproteins. These include both inorganic zinc coordination complexes and small zinc binding peptides. These data have been analyzed to determine the extent to which Zn XAFS can be used to determine reliably the ligation environment of the zinc. Because Zn-N and Zn-S XAFS oscillations are nearly out of phase over the accessible energy range, it is difficult to determine the relative number of sulfur and nitrogen scatterers, and in some cases, it is even difficult to determine whether a low-Z (N or O) ligand is bound in the presence of high-Z (S) ligands. We describe a protocol that, by controlling the number of variable parameters, can be used to obtain an accurate quantitation of the number of low-Z ligands. We also show that two of the variables that are often treated as freely adjustable parameters, the scale factor and shift in the,threshold energy, can lead to erroneous results if not carefully controlled.