There has been a lot of work about how enzymes work at the atomic level. Most studies have used x-ray crystallography (and increasingly NMR spectroscopy and electron microscopy) to determine the three-dimensional structures of enzymes at atomic resolution. These pictures of enzymes can help reveal which parts of the enzyme are involved in performing catalysis and reveal regulatory mechanisms. Using these enzyme structures, biologists can then study enzyme catalysis computationally using molecular dynamics or other types of computer simulations.
Most biochemistry text books should talk about enzyme catalysis and mention structural studies of enzymes. The Protein Databank (http://www.rcsb.org/pdb) is a repository for atomic resolution structures of proteins, and it's molecule of the month feature talks about many enzymes and how they work.