Figure 2.
Specific binding of c-di-GMP. (a) The J1b/2 region stitches the three-helix junction and provides a nucleotide that intercalates between the c-di-GMP. View from the direction of Fig. 1d. Note alternation of J1b/2 residues between right (P1a/P1b) and left (P2). (b) View of the binding site from the major groove. (c) View from the minor groove. Additional interactions between the Watson-Crick faces of G19 and A47, and the sugar edge of A49 and gII are suggested by the location of hydrogen-bond donors and acceptors (colored blue or red denoting nitrogen or oxygen, respectively), but remain uncertain at the current resolution limit. Dashed lines denote putative hydrogen bonds (distance cutoff=3.8 Å; note that the mean precision of the atomic coordinates is 0.5 Å). In panel (c), the hydrogen bond marked (*) is between the N6 of A18 and the N3 of gI, not between G19 and the c-di-GMP.