Comparison of the GUAA structure (thick lines) with other GNRA tetraloop structures. (A) Stereodiagram of the backbone atom superposition of 20 tetraloop structures determined to at least 2.4 Å resolution (see Materials and Methods); the standard orientation of the tetraloop bases (purple) is contrasted with the altered orientation (green). (B) Two extremes in the conformation of the base pair between the first and the fourth nucleotide of the tetraloop. (C) Stereodiagram of the superposition of the GUAA tetraloop reported here (green) and the other tetraloop structures determined to at least 2.0 Å resolution (see Materials and Methods). The GUAA structure illustrates the altered orientation of the last three bases of the tetraloop whereas the other structures illustrate the standard orientation. In the tetraloop, the pro-Rp oxygen of the third nucleotide (circled) is within 3.2 Å of the first guanine base. Arrows marking solvent-mediated hydrogen bonds are pointing toward proton acceptors. Most of the conserved solvent sites are obligate proton acceptors (asterisks).
