| Id | Element | Ion | Binding family | Amino acids or nucleotide residues names | All bound residues | Is homomer | Number of bound amino acids or nucleotide residues | Number of all bound residues | Number of coordinating chains | Representative |
|---|---|---|---|---|---|---|---|---|---|---|
| 2GVH-NA-1 | NA | Na⁺ | D3 | ASP. | ASP. | ✔ | 3 | 3 | 3 | ✔ |
| 5I96-CA-2 | CA | Ca²⁺ | D3 | ASP. | ASP.HOH. | ✔ | 3 | 6 | 2 | ✔ |
| 6X9H-NA-1 | NA | Na⁺ | D3 | ASP. | ASP. | ✔ | 3 | 3 | 3 | ✔ |
| 6VFZ-CA-1 | CA | Ca²⁺ | D3 | ASP. | ASP.HOH. | ✔ | 3 | 6 | 2 | ✘ |
| 6VFZ-CA-2 | CA | Ca²⁺ | D3 | ASP. | ASP.HOH. | ✔ | 3 | 6 | 2 | ✘ |
| 7CFS-NA-1 | NA | Na⁺ | D3 | ASP. | ASP. | ✔ | 3 | 3 | 3 | ✘ |
| 1VEL-CD-1 | CD | Cd²⁺ | D3 | ASP. | ASP.GLU.HOH. | ✔ | 3 | 3 | 3 | ✔ |
| 1VEL-CD-2 | CD | Cd²⁺ | D3 | ASP. | ASP. | ✔ | 3 | 3 | 3 | ✘ |
| 1VEL-CD-3 | CD | Cd²⁺ | D3 | ASP. | ASP. | ✔ | 3 | 3 | 3 | ✘ |
| 1VEL-CD-4 | CD | Cd²⁺ | D3 | ASP. | ASP. | ✔ | 3 | 3 | 3 | ✘ |
| 4N4N-K-1 | K | K⁺ | D3 | ASP. | ASP.HOH. | ✔ | 3 | 4 | 3 | ✔ |
| 4N4O-K-1 | K | K⁺ | D3 | ASP. | ASP.HOH. | ✔ | 3 | 4 | 3 | ✘ |
| 4G3P-CO-1 | CO | Co²⁺ | D3 | ASP. | ASP. | ✔ | 3 | 3 | 3 | ✘ |
| 4QQO-MG-1 | MG | Mg²⁺ | D3 | ASP. | ASP. | ✔ | 3 | 3 | 3 | ✔ |
| 4QQO-MG-2 | MG | Mg²⁺ | D3 | ASP. | HOH. | ✔ | 3 | 6 | 3 | ✘ |
| 2QFX-CA-2 | CA | Ca²⁺ | D3 | ASP. | AKG.ASP. | ✔ | 3 | 4 | 2 | ✘ |
| 2MPR-CA-1 | CA | Ca²⁺ | D3 | ASP. | ASP. | ✔ | 3 | 3 | 3 | ✘ |
| 2ID3-CA-2 | CA | Ca²⁺ | D3 | ASP. | ASP.HOH. | ✔ | 3 | 6 | 2 | ✔ |
| 2ID3-CA-3 | CA | Ca²⁺ | D3 | ASP. | ASP.HOH. | ✔ | 3 | 6 | 2 | ✘ |
| 4L03-CA-1 | CA | Ca²⁺ | D3 | ASP. | AKG.ASP.HOH. | ✔ | 3 | 6 | 2 | ✔ |