This is a follow-up to my earlier question here How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center? about the lactate synthase. I am using the lactate synthase and the paper I referenced only as an example. But sadly, it's not a great example because the authors have not submitted their (predicted) model of the exact ligand configuration during the critical catalytic step when actually the Galactose is added at beta-configuration to the Glucose.
I would like to find another example which of an enzyme, perhaps involving a metal ion too, for which we have pretty exact configurations submitted to PDB that show how exactly the reactants are aligned to create a specific reaction with a specific stereo-configuration, so we can see why exactly the reaction occurs on that atom and in that direction.
I thought the glycolysis pathway should be very well understood by now, but when I went to UniProt KB looking for the hexokinase, I do not see any tertiary structure model with any ligand. Besides, the glycolysis is a catabolic pathway, and I'd like to show an anabolic reaction, although if I remember correctly, many of the glycolysis steps are reversible.
Appreciate if you can point me to better examples that have lots of "snapshots" of the reaction publicly available.
This is what I am looking for: an anabolic enzymatic reaction, ideally with a metal ion involved in the reaction complex, and for which -- unlike in the case of the lactate synthase -- we have snapshots for the critical step of the reaction: the alignment of two ligands which get bonded into a single stereo-isomer. There is nothing dumb, nothing too broad, and nothing opinion-based about this question. The truth is, it's hard to find one by just trial and error fishing on PDB or UniProt.