I don't think there is a problem with changing them, but you will rarely ever come across this phrase in speaking or writing.
Usually we say something like:
"It's not in my nature to do so" or "It's not in my nature".
I have never heard this before: "You don't have it in your nature to be so."
But I don't think it's incorrect to say but extremely rare to come across.
I usually come across: "You don't have what it takes to be so" and "You don't have it in you to be so".