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I think you need to say that Mommy doesn't HAVE a penis. Boys have penises, girls have vaginas. I don't think you need to get more in depth than that, although you may want to start thinking about how to answer the inevitable questions about babies and the purpose of said penises and vaginas. (And perhaps remind him that this conversation is best had at home, and not at school with teachers or friends, unless you want angry phone calls from his schoolmates' parents.....)
Azriona has it right. Just tell the kid the truth. There's absolutely no evidence supporting the idea that educating your kids about physical gender differences does anything but, you know, educate them. I wouldn't necessarily go so far as to explain how those differences work together, simply because a four year old doesn't have the base with which to really understand what it is you're talking about. Any kid is going to inquire about anything their curiosity presents to them, and that curiosity is quite literally infinite. It's what their built to do, and with rare exceptions, there's not such thing as "TMI".
My first thought was, "why is your son just asking this now?" My daughter knew the difference between mommy's and daddy's anatomy by the time she was 3, although the question was probably asked as "what's that?" And I'm certain this was before her little brother (39 months younger) was born. I'm guessing you might be a single mother?