|
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).
|
