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Where can I find a list of enzyme cofactors and/or co-enzymes, ordered by how common they are?
For example, $O_2$, $H_2O$, $ATP$, $ADP$, $NAD$, should be ranked in the first places, because they participate in most reactions.
Check this out. This resource lists organic cofactors and the associated enzymes. See the wikipedia page also.
Many metals also serve as prosthetic groups in enzymes. They include- Magnesium, Manganese, Iron, Cobalt, Nickel, Copper, Zinc, Molybdenum.
FeS clusters are also an important part in many important enzymes in mitochondria and plastids.
coenzymes are organic molecules that are required by certain enzymes to carry out catalysis.
CoFactor - The organic enzyme cofactor database of EBI