Figure 4. Close-up of several Ca²⁺ binding sites.

The side-chains of nearby residues are shown, with cyan representing carbon, red – oxygen, and blue – nitrogen atoms. The backbone of these residues is also colored by index from red to blue. The yellow balls represent the putative site centers of the Ca²⁺ binding sites as identified by FEATURE, scoring over 50 on global grid FEATURE scanning. A Close-up of the Ca²⁺ binding site located at the active site of the HOLO – APO pair 3DNI – 1DNK The red, blue and green strands illustrate that disparate parts of the molecule come together to form this binding site. 1 1DNK highest scoring conformation is shown. 2 1DNK low scoring conformation is shown. 3 1DNK site as it appears in the original PDB file is shown. 4 3DNI conformation is shown which scores similarly to the highest scoring 1DNK conformation. B Close-up of the CA91 binding site in the HOLO – APO pair 1K96 – 1K8U and the 10 ns result of 1K8U. The single flexible loop illustrated in each panel defines this Ca²⁺ binding site. 1 1K8U highest scoring conformation from the 10 ns MD simulation is shown. 2 1K8U low scoring conformation is shown. 3 1K8U site as it appears in the original PDB file is shown. 4 1K96 conformation is shown which scores similarly to the highest scoring 1K8U conformation.