Bioremediation of toxic metal ions using bacterial strains is a promising tool. Metal binding motifs in microbial proteins are involved in the regulation and transport of such toxic metals for metal detoxification. A bacterial strain designated TWSL_4 with metal (Cu, Cd, and Pb) resistance and removal ability was isolated and identified as a Bacillus megaterium strain using 16S rRNA gene analysis. An operon with 2 open reading frames (ORFs) was identified, cloned, and sequenced. ORF1 and ORF2 were identical to the cadmium efflux system accessory protein (CadC) and cadmium-translocating P-type ATPases (CadA) of B. megaterium strain YC4-R4 respectively. A protein homology search using Swiss model retrieved no crystal structures for CadC and CadA of Bacillus sp.. CadC of TWSL_4 had a sequence identity of 53% to the CadC (121aa) protein and 51.69% to the CadC crystal structure (1U2W.1.B; GMQE=0.75) of Staphylococcus sp. pI258. Molecular dynamic simulation studies revealed the presence of three metal binding regions in CadC of TWSL_4, [ASP7-TYR9], [ASP100-HIS102], and [LYS113-ASP116]. This is the first report showing evidence for the presence of Cd2+ and Zn2+ metal binding motifs in the CadC regulator of the Bacillus megaterium cad operon. The bacterial strain TWSL_4 was also found to contain two different P type ATPases encoding genes, cadA and zosA involved in metal resistance. Furthermore, the metal bioremediation potential of strain TWSL_4 was confirmed using an industrial effluent.