Figure 2.

The surface electrostatic potential maps of P5b (PDB:1AJF) helix and P5 (PDB:1C0O) helix of Group I intron with the bound cobalt hexamine shown as a stick representation. (A) Potential maps were computed using non-linear PBE approach as described in the Methods. (B) Potential maps were computed using linear PBE approach. Enhanced definition of the region of negativity in the major groove of the map shown in (A), which permits greater acuity in identification of the metal ion binding site, is the result of use of the non-linear PBE. The color scheme used in this map is as follows: yellow is the most negative (−6.8 kT/e) and green is the most positive (1.7 kT/e). White is neutral. Red and blue represent negative and positive electrostatic potentials, respectively.