Often in logic and model theory structure means Signature [see Structure (Mathematical logic)].
See e.g. Dirk van Dalen, Logic and Structure page 58:
A structure is an ordered sequence $\langle A,R_1,\ldots, R_n,F_1,\ldots,F_m,\{ c_i \mid i \in \} \rangle$, where $A$ is a non-empty set [the domain]. $R_1,\ldots,R_n$ are relations on $A$, $F_1,\ldots,F_m$ are functions on $A$, the $c_i$ are elements of $A$ [the constants].
So, we have a domain of individuals: the set $A$, and relations and operations on them.
Note that in this sense a signature is related only to the language.
The Bourbaki-like term "Mathematical structure" is usually used not in conenction with a formal language, but considering more specifically the relavnt axioms: this is IMO the sense of Wiki's statement "a structure is a set endowed with some additional features on the set (e.g. an operation, relation, metric, or topology)."
There is no contradiction, because operations and metrics are functions; also a topology is a function from the space $X$ (the domain of the structure) to the collection of subsets of $X$.