Here are some scripts to help you with the questions above. To use them, first start a desktop copy of RasMol. Then click to download the .pdb file. Then, to see each view described, click the appropriate .spt file. Excerpt of the PDB file 1as9, containing only citrate, the FeS cluster, and atoms within 6 angstroms of them.
Sulfur atoms are yellow, iron atoms orange.
Also note the Fe closest to citrate. This ion is complexed with a citrate carboxyl and the substrate water molecule. It is clear from this view that aconitase can distinguish the two carboxymethyl groups of citrate. Because this complex is catalytically active, it is not possible to determine its structure by crystallography. 1CME is a theoretical model built from a crystallographic model of MDH bound to citrate, which binds in similar fashion to malate.