Jim is correct. No Atlas II ever flew without a sustainer engine, but
Atlas II did delete the two small side-mounted vernier engines that
were on earlier Atlas vehicles.

General Dynamics was working on a new design called Atlas IIAR, that
would have replaced the booster/sustainer MA-5A engine with a straight
two-chamber design. Rocketdyne bid an engine design. So did Russia's
Energomash (in combo with Pratt). Energomash won when Rocketdyne
pulled out of the competition. Eventually, General Dynamics space
division was sold to Martin Marietta, which was later merged into
Lockheed Martin - and the new Atlas IIAR was renamed "Atlas III".
Lockheed used the new Atlas as the starting point for its EELV design -
which it called "Atlas V". Next year, the last Atlas III will fly and
Lockheed will shut down the last remnants of the long-running
Convair/General Dynamics heritage Atlas program at the Cape.

- Ed Kyle