Is it the birth certificate, voter's registration, social security, or more? What common binding of contracts or agreements, in this free country, allows one sovereign (the state) to assume authority over another sovereign (a natural person)?
The source of the power of the United States government to do the things that it does are the people themselves. (United States Constitution)
The people have decided on three branches of government (judicial, executive, and legislative). The expression of the will of the people through these three branches of government results in the government having authority to enforce laws within the borders of the United States.
It is not through any contract, agreement, certificate, registration, or other that you come under the jurisdiction of the United States, but simply by your presence. (There are some limited exceptions for foreign diplomats and tribal sovereignty.)
Why you are not sovereign
In the first place, you are not sovereign. Sovereign means:
A chief ruler with supreme power; one possessing sovereignty. (q.v.) It is also applied to a king or other magistrate with limited powers.
In the UK, the sovereign is the monarch, currently Queen Elizabeth II. In Australia and Canada it is Queen Elizabeth II's representative, currently Peter Cosgrove and David Johnston respectively. In the USA it is the President, currently Barak Obama. And so on ...
Perhaps, you are thinking of a sovereign state? Well, you're not one of those either:
a state which administers its own government, and is not dependent upon, or subject to, another power.
In fact, you are not even a non-sovereign state, like New South Wales, Ottawa, Scotland or South Carolina:
A federated state is a territorial and constitutional community forming part of a federal union.
Why sovereign's have authority over you
Because they have "supreme power" or "limited powers"; and you don't.