The fructose 1,6-bisphosphate aldolase (FBA) is important for both glycolysis and gluconeogenesis in life. Class II (zinc dependent) FBA is an attractive target for the development of antibiotics against protozoa, bacteria, and fungi and also widely used to produce various high-value stereoisomers in the chemical and pharmaceutical industry. In this study, crystal structures of class II Escherichia coli FBA (EcFBA) were determined from four different crystals with resolutions between 1.8 Å and 2.0 Å. Native EcFBA structures showed two separate sites of Zn1 (interior position) and Zn2 (active site surface position) for Zn2+ ion. Citrate and TRIS bound EcFBA structures showed Zn2+ position exclusively at Zn2. Crystallographic snapshots of EcFBA structures with and without ligand binding proposed the rationale of metal shift at active site, which might be a hidden mechanism to keep the trace metal cofactor Zn2+ within EcFBA without losing it.