Depends on what kind of ATX mobo it is, as there is Extended-ATX. What exact case are you looking into? The cases themselves should say they support certain ATX motherboards - for example it might say EATX, ATX, MATX support.
The case should state which boards it does support. Heck a bunch of them will even have the mounting points inside the case labeled for the board/standard for that hole. I haven't worked with a Mid Tower that I can remember that doesm't support ATX but it is always good to check to make sure.
Try a Corsair Carbide 400R. I have it... its great. very easy to get in and out of, good airflow, good fans, short height to fit under the desk, and i have an ASRock Extrem4 Gen3 with a big @ss Thermaltake FRIO but i know it can fit most water cooling options.