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
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