Fig 1.
Atom preferences in nickel coordination.
Figure represents a) the various atom types coordinating with the Nickel and b) shows the interactions distances of atoms with the metal.
Table 1.
Fig 2.
Coordination geometries in penta and tetra-residue chelates.
Fig 2a and 2b show the penta-residue coordination towards Nickel displaying a square pyramidal geometry with HHHHH chelate and an octahedral geometry with HHEHM chelate. The bi-dentate coordination of glutamic acid at n+ 21 positions is observed through the coordination of its ε- oxygen atoms. Fig 2c-2j displays the tetra- peptide coordination of nickel. Residue positions are labeled in the figure where, ‘n’ represents the position of the first residue in the chelate and the following number indicates the distance of successive residues relative to the initial residue of the chelate. The letter ‘m’ denotes the position of a residue if separated by a distance >100 residues. The coordinating residues are displayed as sticks and as cartoon to highlight the secondary structures. The atom coloring represents carbon (green), nitrogen (blue), oxygen (red) and sulphur (yellow). Nickel atom is shown as sphere and colored in grey.
Fig 3.
Coordination geometries in tri-residue chelates.
The figure shows the dominating coordinating patterns among the tri-residue chelates. Fig 3a-3d shows cysteine based chelates. Fig 3e and 3f shows the different geometries among DDD chelates. Fig 3g and 3h display the secondary structural differences among HHH chelates. Fig 3i, 3j and 3k represent the coordination of aspartic acid and glutamic acid in association with histidine. Fig 3l, 3m, and 3n show the identical coordination pattern of residues spaced at a distance of 1 residue length. Residue positions are labeled in the figure where, ‘n’ represents the position of the first residue in the chelate and the following number indicates the distance of successive residues relative to the initial residue of the chelate. The letter ‘m’ denotes the position of a residue if separated by a distance >100 residues. Coordinating residues are displayed as sticks and as cartoon to highlight the secondary structures. The atom coloring represents carbon (green), nitrogen (blue), oxygen (red) and sulphur (yellow). Nickel atom is shown as sphere and colored in grey.
Fig 4.
Coordination geometries in bi-residue chelates.
The figure shows the dominating patterns among the bi-residue chelate. Residue positions are labeled in the figure where, ‘n’ represents the position of the first residue in the chelate and the following number indicates the distance of successive residues relative to the initial residue of the chelate. The letter ‘m’ denotes the position of a residue if separated by a distance >100 residues. Coordinating residues are displayed as sticks and the atom coloring represents carbon (green), nitrogen (blue), oxygen (red) and sulphur (yellow). Nickel atom is shown as sphere and colored in grey.
Table 2.
Probabilities of amino acid occurrence.
Table 3.
Putative amino acid positions for nickel coordination.
Table 4.
Probable nickel binding motifs from group of bacterial and archeal species.