I found out that my best friend is an Atheist!!!! What should i do???

Why should it matter to you? He doesn't believe the same thing you do on one topic (religion). If you limited yourself to only making friends with people who agreed with you on everything, you'd spend a lot more time alone. You've described this guy as dependable, loyal, smart, and kind. Those things are far more important qualities in a friend than their religion, aren't they? Just keep being his friend.