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Trivalent holmium ions were shown to isomorphously replace magnesium ions to form an ADP-2Ho complex in the nucleotide-binding domain of Bacillus subtilis 5-methylthioribose (MTR) kinase. This nucleotide–holmium complex provided sufficient phasing power to allow SAD and SIRAS phasing of this previously unknown structure using the LIII absorption edge of holmium. The structure of ADP-2Ho reveals that the two Ho ions are approximately 4 Å apart and are likely to share their ligands: the phosphoryl O atoms of ADP and a water molecule. The structure determination of MTR kinase using data collected using Cu Kα X-radiation was also attempted. Although the heavy-atom substructure determination was successful, interpretation of the map was more challenging. The isomorphous substitution of holmium for magnesium in the MTR kinase–nucleotide complex suggests that this could be a useful phasing tool for other metal-dependent nucleotide-containing proteins.

Supporting information

PDB reference: MTR kinase–ADP-2Ho complex, 2olc, r2olcsf


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