Fig. 2

Localization of potassium ions in the 70S ribosome decoding center. a Structural rearrangements of the decoding center and its stabilization by potassium ions upon binding of A-tRNA. In the initiation complex (left), only one K⁺ ion conserves the architecture of decoding center through coordination with C518 and G529 of h18 and amino acid residues Pro45 and Asn46 of protein uS12. The mRNA in the initiation complex in the absence of A-tRNA is shifted away from h18, while G530 adopts energetically unfavorable syn conformation. In the elongation complex (right), in contrast, mRNA is moved towards h18 in order to form base pairing with the A-tRNA. In this scenario, an additional K⁺ ion is involved in the stabilization of codon–anticodon interaction via coordination through C518, G530 (in anti-conformation), Pro45 and U(+6) ribose. b, c The best fitting coordination geometry was estimated to be square antiprism (coordination number 8) with an RMSD of 0.261 Å for the five identified coordinating atoms positions for the “first” K⁺ ion in the decoding center (b, left), and bi-capped square antiprism (coordination number 10) with RMSD of 0.319 Å for the five identified coordinating atoms positions for the “second” K⁺ ion in the decoding center (c, left). In silico modeling shows that Mg²⁺ ion does not fit into these binding pockets due to its distance and geometry constrains (b, c right). 16S rRNA elements are shown in yellow, nucleotides A/U(+6) and G530 are highlighted by light blue circles. Contacts between K⁺ and ribosomal components are shown in round dash, U(+6)-G34 base pair is marked by long dash lines, two K⁺ ions are marked with white star (“first” K⁺) and black star (“second” K⁺)