One of the best ways that I have found for modeling reaction pathways is to set up a boolean network for that specific pathway. The boolean will give you an idea of the possible different states in that pathway (dependencies) and while not really necessary I find it helps orient you to the system.
The next step once you have yourself oriented is to set up Michaelis-Menton equations which you can then use to run you ODEs. Here is a great primer on how to set up these equations: http://depts.washington.edu/wmatkins/kinetics/michaelis-menten.html
The subsequent modules provided in that link are also helpful in explaining how to set-up quadratic velocity equations and do different sequential models.
Also, I'm sure you know this but, it bears saying: these are all steady-state kinetics. If you are looking for a more accurate model of what is occurring in that reaction you are going to have to set-up stochastic models of your system.
Hopefully, that answers you question. Good luck!
EDIT
I have found a paper that seems to relavent to the process you are trying to model. It goes into a bit more detail than I think you are looking for but the basics seems sound. Mendoza-Cozatl and Moreno-Sanchez, 2006