Monatomic Ion Coordination in Proteins

In order to understand the role of ions in proteins, it is important to have an accurate description of the interactions between bound ions and atoms common in proteins. An automated analysis method was developed to analyze monatomic ions contained in crystal structures in the RCSB Protein Data Bank (PDB). The coordination characteristics of the most prevalent monovalent cations in the PDB were analyzed through the radial distribution functions of oxygen atoms around ions. It is known that sodium ions coordinate oxygen atoms within about a 6 \AA \ radius, with a clear first “coordination shell,” similar to a hydration shell in bulk water, and a secondary shell also typically visible. However, oxygen atoms are not the only atoms that can coordinate cations, and coordinating atoms for anions are far less understood than those for cations. The analysis was extended to explore the distributions of other coordinating atoms, namely nitrogen, sulfur, and carbon, as well as anions and multivalent cations. It was observed that many ions are preferentially coordinated by certain atoms, for example, zinc specifically is largely coordinated by sulfur. Additionally, quantitative values were calculated to describe the locations and strengths of the coordination shells for each ion.