Effect of metal ion on the structure and function of LiPDF: The study of the fine structure around the metal site using XANES

We used X-ray absorption near edge structure (XANES) spectroscopy to investigate the metal-dependent enzymatic activity of the peptide deformylase from Leptospira interrogans (LiPDF). Ab initio full multiple scattering calculations performed by MXAN are applied to obtain the local structure of the cobalt-containing LiPDF (Co-LiPDF) and zinc-containing LiPDF (Zn-LiPDF) around the metal sites in pH9.0 buffer solution. The result shows the cobalt-wat1 (the bond water molecule) distance of Co-LiPDF is 1.89 Å, much shorter than that of Zn-LiPDF, 2.50 Å. That is an essential factor for its low catalytic activity.