relative clauses問題

First of all, your sentence should be written as follows using the relative pronoun [which]:

Japan, which is famous for animated movies, is a wonderful country.

Here, the relative pronoun [which] is used to replace the pronoun [It] in your second sentence (which refers to Japan). If you want to use [where], you may write something like this:

Japan is a wonderful country where there are famous animated movies.

Here, [where] = [in which] = [in this country (Japan)]

For non-defining relative clauses, comma(s) is/ are narmally needed. Unless the relative clause comes at the end of a sentence, two commas are necessary.

Examples
- Japan, which is famous for animated movies, is a wonderful country. (2 commas)
- This is Mr. Rogers, who's joining the firm next week. (1 comma)

Hope that it can help you.