Fig. 1.

Metal ions assignment in T. thermophilus 70S ribosome on the example of elongation complex. a Thermus thermophilus 70S EC represents the elongation state of the ribosome that contains poly-U mRNA with SD sequence and three cognate tRNA^Phe in the A-, P- and E-sites. Parts of the central protuberance and the 30S head are omitted for clarity. Abbreviations used: PTC peptidyl transferase center, DC decoding center, SD Shine-Dalgarno. b Thermus thermophilus 70S elongation complex (PDB ID 4V6F) was used as an initial model for ions re-assignment. The same complex was crystallized and data were collected at beamline I23 (Diamond Light Source, UK) at two different wavelengths (3.542 and 3.351 Å, which correspond to energies below and above the K-absorption edge of potassium). Electron density from three independent datasets collected at different wavelengths (1.000 Å (PDB ID 4V6F), 3.542 and 3.351 Å) were used to build an atomic model, which contained 211 experimentally distinguished K⁺ ions, 334 Mg²⁺, 251 Mg(H₂O)₆²⁺, 1 Zn²⁺ and 1 Fe₄S₄ cluster in place of 3255 Mg²⁺ and 3 Zn²⁺ ions assigned previously. c, d Distribution of K⁺ and Mg²⁺ ions within 70S ribosome and each individual subunit. Potassium ions are coordinated in intersubunit bridges B2a and B2c (c). One magnesium ion is coordinated in B2c bridge (in the IC magnesium ion has slightly different position and coordinated via water molecules) (d). OMC stands for 2′-O-methylcytosine. K⁺ ions colored in magenta, Mg²⁺ ions in green, solvent shell shown in red, Zn²⁺ in dim gray, in Fe₄S₄ cluster in iron colored in gray and sulfur in black. Small ribosomal subunit (30S) parts colored in yellow, large subunit (50S) components in blue. Intersubunit bridges are shown in bright yellow and bright blue. For clarity, ions within ribosome are shown in sphere representation with increased van der Waals radius. Additionally, tRNA and mRNA ligands are omitted from the interface of 30S subunit in c and d