Tyrosylprotein sulfotransferase-2 catalyses important, but a less explored posttranslational modification of proteins. The crystallographic structure of the full complex, containing the enzyme, PAPS cofactor and the peptide substrate (WTFC) revealed important structural and atomistic details about the overall structure, binding sites and interactions in TPST-2, but is not informative about the conformational flexibility, which is a fundamental protein property. In a recent computational study we analyzed the impact of conformational flexibility on key geometric determinants and interactions in WTFC. However, there are still unexplained effects about how the conformational dynamics influences the formation of the catalytically active dimer form of the enzyme and also how the binding of the cofactor and the substrate to the apoenzyme influences the structure and the pattern of correlated motions in the enzyme. In order to provide the missing knowledge we performed a molecular dynamics study on the dimerization mutant W113A, the apoenzyme (APO), enzyme–cofactor complex (ES), and enzyme–substrate complex (ES) and compared the results to the WTFC. We identified new hydrophobic interactions important for the stabilization of the enzyme dimer and provided structural insight about the role of the key mutation W113A for the dimerization in the absence of experimentally-derived structure. In addition we showed that the binding of the substrate and cofactor to the apoenzyme contributes to the stability of the whole active complex, influences the local interactions in the binding site and importantly, affects the pattern of the correlated motions in the entire molecule.