Figure 2 - full size



	Figure 2 - full size

Figure 2.
Figure 2. Protein -RNA contacts. a, Stereo diagram of the cfos-11 structure and HuD1,2 side chain contacts. b, Stereo diagram of the TNF 11 structure and HuD1,2 side chain contacts. The structures of the cfos-11 and TNF 11 RNAs are shown as ball-and-stick models colored by atom type. The bases and 5' and 3' ends of the RNA and side chains contacting the RNA are labeled. 2F[o] - F[c] maps for the cfos-11 and TNF 11 RNAs contoured at 1 are shown superimposed on their respective ball-and-stick models. Two water molecules are shown as green spheres. Hydrogen bonds within the RNA structures and with the water molecules are shown as black dotted lines and hydrogen bonds between the protein and RNAs are shown as red dashed lines. Amino acid residues are colored as in Fig. 1b. c, Summary of contacts between HuD1,2 protein and cfos-11 RNA. d, Summary of contacts between HuD1,2 protein and TNF 11 RNA. Red lines indicate side chain contacts, green lines indicate main chain contacts, and dashed orange lines indicate stacking interactions. Distances in Å are noted. Atoms on the RNA that are recognized in water-mediated contacts are highlighted with yellow. In the complex with TNF 11, the side chains of Tyr 128, Arg 166 and Lys 201 and the main chain of A203 seem to have moved away from the RNA to accommodate the A3 base. This could indicate plasticity in this site or reflect the ability to accommodate a less than ideal sequence at the concentration used for crystallization (1 mM).