Space Constrained Homology Modelling: The Paradigm of the RNA-Dependent RNA Polymerase of Dengue (Type II) Virus
Figure 5
Closeup of the ssRNA (upper) and the UTP/Mn++ (lower) sites in (a) the dengue polymerase model produced by the 3D space-aided approach and (b) the Dengue X-ray polymerase structure, for comparison (PDB entry: 2BMF). Coordinates of the substrates were copied to the model from the template structure (see text). The substrates are depicted in sticks and dotted spheres, whereas spheres in magenta represent the catalytic Mn++ atoms. Invariant residues (labeled) of various motifs in the vicinity of either substrate are structurally conserved in this Dengue polymerase model demonstrating the efficiency of the novel approach as opposed to the conventional homology modeling.
