Mineral deposition is essential for the development of hard tissues like bone and teeth. In matrix-mediated mechanisms responsible for dentin formation, type I collagen defines the framework for mineral deposition and by itself is not sufficient to support nucleation of hydroxyapatite. However, in the presence of non-collagenous proteins, nucleation sites have been identified within the hole regions of the fibrils, and at these sites, mineral crystals can grow and propagate. Non-collagenous proteins constitute 5-10% of the total extracellular matrix proteins. They are embedded within the mineral deposits, suggesting a possible interaction with the mineral phase. During dentin formation, phosphophoryn (PP), an abundant macromolecule in the extracellular matrix, can initiate mineral deposition in localized regions by matrix-mediated mineralization mechanism. In our work, we have demonstrated that PP, due to its highly phosphorylated post-translational modification, can bind calcium ions with high affinity and at the same time aggregate collagen fibrils at the mineralization front. Molecular modeling has further demonstrated that the spacing of the carboxyl and phosphate groups present on PP might be essential for dictating the crystal orientation relative to the collagen substrate. Thus, PP may provide the interface linkage between mineral crystal and collagen fibrils.