Glutamine, hydrogen-bonding interactions

The new crystal structure of the ribosome—RFl complex sheds more light into the interactions between the GGQ motif and the peptidyltransferase center. This complex represents the product state of peptide release since a deacylated tRNA is bound to the P site. Importantly, the main chain amide of the conserved glutamine hydrogen bonds to the 3 OH of A76 in the P site, which is the leaving group of the hydrolysis... 

Q Hydrogen-bonding interactions between glutamine and adenine. 

Asparagine and glutamine residues constitute only 6% and 2% of the Ca -coordinating ligands in the sites of Table II. In theory the amide side chains of these amino acids can provide one oxygen for unidentate coordination to Ca as well as interaction with hydrogen-bond donors ... 

Next, the authors explored the 02 mechanism. In this case, the largest model used (15) involved two methylammonium ions and two formate ions to mimic the Lys-Asp-Lys-Asp tetrad, and an acetamide hydrogen-bonded to a water, which interacts with 02, to mimic a glutamine-water bridge found in the Wu-Pai crystal structure.22... 

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