I am using Python to create an RSA encoding system but I have to follow some conditions: 

Both of private and public keys have to be encoded in 16 values.
The keys has to be encoded in 64 bits.

I wanted to used PyCryptodome, but since it limit you to use a size of 1024 bit, or more and for my case I just want to encode them in 16 values.
As mentioned in the comments by me: 16 x 64 = 1024, and 1024 is an often used RSA key size.
I strongly suggest that you are misunderstanding the question. It seems you have to perform 1024 bit modular exponentiation using machine words of 64 bit internally for the calculations. How the keys are encoded is an entirely other matter; during the calculations you'd use the modulus and exponent as an unsigned number after all, not the encoded key.
With RSA there are three distinct key "sizes" possible:

the key size, which is just the size of the modulus as unsigned number in bits;
the encoded key size of the public and private key, which can be any size but is commonly larger than the  key size mentioned above;
the key strength, which is the strength of the key compared to e.g. an AES key.

Note that RSA with a key size of 1024 has a comparative strength of 80 bits, which is considered on the low side of things.
can I generate a fixed encrypted message of 16 values in Python