Evaluation of the (haem)Fe—N∊2(HisF8) bond distances from haemoglobin structures deposited in the Protein Data Bank

Abstract

Scientists working on the structure and function of proteins use haemoglobin as a model of allosteric proteins. In this molecule, the (haem)Fe-N(2)(His) bond is one of the most significant because the length of this bond provides relevant information about the mechanism of cooperativity and affinity for O(2). Thus, the aim of the present study was to evaluate the quality of the structural models of Hb deposited in the Protein Data Bank (PDB), in particular the reliability of the Fe-N(2) bond distance. To achieve this, 329 Hb structures solved by X-ray diffraction were downloaded from the PDB. The Fe-N(2) bond distance was computed and compared with the ideal value determined using the spectroscopic techniques of X-ray absorption and EXAFS. This investigation showed the presence of crystallographic structures of native haemoglobins deposited in the PDB in which the Fe-N(2) bond distance was far beyond the ideal value found for this length, a fact that makes their use in studies that correlate haemoglobin structure and function questionable.