Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system

Active site density in the kinase•ATP•Mg²⁺ and kinase•ADP•Mg²⁺ complexes. Stereoviews of the finely sampled electron density maps of the active sites of the A protomers of the SeMet-kinase (panel A; 2.0 Å) and native kinase (panel B; 2.1 Å) crystals. The red mesh depicts F_o − F_c difference density (contoured at 3.0 σ; grid spacing 0.13 Å) calculated prior to the inclusion of nucleotide or a metal complex in the model. The difference density was modeled as ATP•Mg²⁺ for the SeMet-kinase structure and ADP•Mg²⁺ for the native kinase structure. The nucleotides are depicted as stick models with gray carbons; Mg²⁺ is shown as a magenta sphere. The contacts to the ligands of the octahedral Mg²⁺ coordination complex are denoted by dashed lines. Waters in the metal complex are red spheres. The gray mesh depicts the refined 2F_o − F_c density maps (at 1.5 σ; grid spacing 0.13 Å) of P-loop residues Lys21, Ser22, and Thr23 and lid residue Arg120 that are situated close to the ATP/ADP nucleotides.