I think you have your articles mixed up in both sentences. Try these:
A is a (or the) property of the system that regulates the concentration of sodium ions.
The system that regulates the concentration of sodium ions includes property A.
Property A is the property of the (or a) system which regulates the concentration
of sodium ions.
Property A regulates the concentration of sodium ions in the (or a) system.
I think it depends on whether you have several properties in the system, or several systems which include different properties, or several systems that all included property A. If you say a system then there could be several possible systems and property A could be specific to that one system or other systems. If you say the system then that might be the only system for regulating sodium ions. If you say a property A then you are saying one property of the system functions as the regulator. Normally we do not use a in front of a specific property. Instead we say the property A regulates... or just Property A regulates... If I were writing the lab report, and there was more than one possible system I would write:
Property A regulates the concentration of sodium ions in this system.
I was careful to designate a specific system with the word this. I would not say this is the only property that regulates..., because I might not be correct if I am a beginning lab student.