Table 1. Summary of selected cofactors within structures deposited in the PDB archive (June 2010).
Prototypical protein example | Cofactor or chromophore | λmax (nm) | Typical ∊ (mM−1 cm−1) | PDB ligand ID or name | No. of PDB structures |
---|---|---|---|---|---|
Aspartate aminotransferase | Pyridoxal-5′-phosphate | 350, 412 | 6.6, 9.5 | PLP | 568 |
Lactate dehydrogenase | NAD(H) or NADP(H) | 340 | 6.2 | NAD, NDP, NAP | 1480 |
Dihydrofolate reductase | Pterin | 350 | 4.5 | Pterin | 242 |
p-Hydroxybenzoate hydroxylase | FAD or FMN | 450 | 11 | FAD, FMN, flavin | 1466 |
Myoglobin | Heme | 409 | 170 | Hem | 2262 |
Mn superoxide dismutase | Mn(III)-O/N | 480 | 0.91 | Mn | 1395 |
Rubredoxin | Fe (non-heme) | 430–500 | 3–5 | Fe | 766 |
Ferredoxin | Fe2/S2 cluster | ∼400 | 30.6 | FeS | 304 |
High potential iron protein | Fe4/S4 cluster | ∼400 | 15 | SF4 | 388 |
Methylmalonyl-CoA mutase | Co or B12 | 360 | 27.5 | Cobalt | 355 |
Urease | Ni(II)-O/N | 407 | 0.21 | Nickel | 461 |
Azurin or plastocyanin | Cu | 600 | 5 | Cu | 752 |
Photosynthetic reaction center | Chlorophyll | 465, 665 | >100 | BCL, BPH, etc. | 147 |
Bacteriorhodopsin | Retinal | 480 | 27 | Ret | 111 |
Green fluorescent protein | Post-translation modification | 350–700 | 6–94.5 | Luminescent proteins | 218 |