Ion site prediction in YASARA

YASARA Structure can predict binding sites for metal ions in protein structures and other molecules. The approach works by putting a fine grid over the protein and summing up the binding contribution of surrounding oxygen atoms at each grid point, considering ion specific parameters[1,2]. Grid points that exceed a certain threshold are shown in green (weak binding) to white (very strong binding).

The example on the right side shows predicted Ca⁺⁺ binding sites in PDB file 2F3Y (Calmodulin). Four Ca⁺⁺ sites are found, marked with yellow arrows. These match the actual calcium binding sites exactly (shown below).

The approach works best with divalent ions like Ca⁺⁺ or Mg⁺⁺, which exhibit a stronger signal than monovalent ions like K⁺ [3]. The potential involvement of nitrogen and sulfur atoms (histidine, cysteine) is not considered yet.

R E F E R E N C E S

[1] Empirical parameters for calculating cation- oxygen bond valence
Brown ID, and Wu KK (1976) Acta Crystallogr. Sect. B Struct. Sci. 32,1957–1959
[2] Predicting Ca(2+)-binding sites in proteins.
Nayal M and Di Cera E (1994) Proc. Natl. Acad. Sci. U.S.A. 91,817–821
[3] A Conformation-specific interhelical salt bridge in the K+ binding site of gastric H,K-ATPase Koenderink JB, Swarts HGP, Willems PHGM, Krieger E and De Pont JJHHM (2004) J. Biol. Chem. 16,16417-16424