Why can oxygen have a coordination number of 3 in a complex between silver and SiO2? I am running an MD simulation of silver with $\ce{SiO2}$. Initially, my silver atom is neutral and oxygen has a coordination of 2 with silicon having a coordination of 4. After the deposition of silver atoms, I find that the coordination of silver atoms ranges up to 12 and oxygen has coordination of 3 where a bond is formed with silver. Since $\ce{Ag-Si}$ bonds are not present, silicon's coordination number does not change. 

I want to understand why oxygen is able to have a coordination number of 3 as with 2 bonds with silicon, the valency is already satisfied. I know silver forms a fcc-lattice where the coordination number is 12 but I want to get a more in depth detail of this change of coordination number. The basic physics behind it.
High coordination numbers are really not uncommon in solid-state compounds. For example, consider the structure of $\ce{Li2O}$, an anti-fluorite structure. In fluorite proper, calcium ions form a cubic closest packing structure and the fluoride ions occupy the tetrahedral voids. In $\ce{Li2O}$, it is reversed: the oxide ions form a cubic closest packing and lithium occupies the tetrahedral voids. That gives each lithium a coordination number of 4 and by maths and symmetry oxygen must have a coordination number of 8.

Tricoordinated oxide anions are also well-known in solid-state structures. The prime example would be the rutile structure of $\ce{TiO2}$ with hexacoordinated titanium and tricoordinated oxide ions.

In your specific case, the silver cations are acting as Lewis acids while the oxide anions (which have to lone pairs not directed towards neighbouring silicium atoms) can act as Lewis bases. A coordination number of three points to a somewhat covalent (and not so ionic) structure — which makes sense considering significant fragments of $\ce{SiO2}$ are still there.