Figure 4

The guanosine-5′-monophosphate binding site in chain C of PDB entry 1A97 [[34]] is an example of a ligand and binding site flagged as dubious and bad in the PDB, respectively (left panel: upper with cyan ED for the binding site and red ED for the ligand; lower with default view: yellow ED for Dubious and Bad residues), but scored as Good in PDB_REDO (right panel: upper with cyan ED for the binding site and red ED for the ligand; lower with previously bad or dubious residues with orange ED). The RSR and RSCC of the ligand improve from 0.154 to 0.065 and from 0.86 to 0.97, respectively. Two extra hydrogen bonds are introduced, improving the total hydrogen bonding energy from −157 kJ/mol to −199 kJ/mol. The all-atom root mean square deviation of the ligand is 0.6 Å. Of the residues in the binding site, arginine 69 and the boric acid molecule improve most significantly in terms of fit to the ED.