The oxidative photosynthetic carbon cycle reaction is catalyzed by RuBP oxygenase activity:
:RuBP +  → Phosphoglycolate + 3-phosphoglycerate + 2 
During the catalysis by RuBisCO, an activated intermediate is formed (an enediol intermediate) in the RuBisCO active site. This intermediate is able to react with either  or . It has been demonstrated that the specific shape of the RuBisCO active site acts to encourage reactions with . Although there is a significant "failure" rate (~25% of reactions are oxygenation rather than carboxylation), this represents significant favouring of , when the relative abundance of the two gases is taken into account: in the current atmosphere,  is approximately 500 times more abundant, and in solution  is 25 times more abundant than .
The ability of RuBisCO to specify between the two gases is known as its selectivity factor (or Srel), and it varies between species, with angiosperms more efficient than other plants, but with little variation among the vascular plants.
A suggested explanation of RuBisCO's inability to discriminate completely between  and  is that it is an evolutionary relic: The early atmosphere in which primitive plants originated contained very little oxygen, the early evolution of RuBisCO was not influenced by its ability to discriminate between  and .