Figure 2.
Figure 2. (A) Stereo diagram of dimer interface showing the
surface of one monomer and the interacting region from the
adjacent monomer. The surface regions corresponding to the polar
side-chain atoms which bridge the interface are colored: Glu68
OE1 and OE2, red; Tyr130 OH, red; and Arg42 NH1 and NH2, blue.
The box outlines the region shown in B. (B) 2F[o]-F[c] refined
electron density map contoured at 1.5 detailing the
interaction between Arg42 and backbone carbonyls of residues
Phe60' through Ser67' of the dimermate. (C) A-form dsRNA modeled
on the TB nuclease domain so that the scissile phosphates (green
spheres) lie adjacent to the A-site metal ions (yellow spheres).
The 2°-site ions are shown in magenta. The bases forming the
two-nucleotide overhang product are indicated with orange bars.
This arrangement places the minor groove corresponding to the
distal box "anti-determinant" bases (cyan) (Zhang and Nicholson
1997) in close proximity to helices 2' and 5' (red).
Surface electrostatics calculation using APBS (D) (Baker et al.
2001) and surface conservation (E) (Glaser et al. 2003) show
negatively charged and conserved surface residues which align
with the proposed dsRNA binding region.
detailing the
interaction between Arg42 and backbone carbonyls of residues
Phe60' through Ser67' of the dimermate. (C) A-form dsRNA modeled
on the TB nuclease domain so that the scissile phosphates (green
spheres) lie adjacent to the A-site metal ions (yellow spheres).
The 2°-site ions are shown in magenta. The bases forming the
two-nucleotide overhang product are indicated with orange bars.
This arrangement places the minor groove corresponding to the
distal box "anti-determinant" bases (cyan) (Zhang and Nicholson
1997) in close proximity to helices 
2' and