Metal-binding proteins play an important role in maintaining intracellular metal homeostasis and eliminating heavy metal toxification. Many metallothioneins (MTs) have been isolated from mammalian sources, which are a family of low molecular weight metal-binding proteins that are rich in cysteine. However, plants contain a different type of cadmium-binding protein that contain fewer cysteine residues. In this study, cadmium affinity chromatography coupled with laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) has been used to separate and identify cadmium-binding proteins from different parts (root, stem, leaf and grain) of rice (Oryza sativa L.) cultivated under cadmium stress conditions. Seven cadmium-binding proteins with low isoelectric points containing relatively few cysteine residues were chosen for expression in Escherichia coli. The cadmium removal efficiency of protein A3AGZ4 (OsJ_10480) from Escherichia coli △zntA-BL21 was the highest (57.35%), which compares favorably with the cadmium removal efficiency of metallothionein MT (48.99%, mt from mouse,) and SMT (55.84%, smt from Sinopotamon honanense). In addition, for the strain A3AGZ4-△zntA-BL21, most of the bound cadmium was found to accumulate in the cytoplasm and not the cell wall. These results indicate that these plant proteins can bind cadmium to reduce heavy metal toxicity, thus contributing towards bioremediation of cadmium in the environment.