It is because of Japanese culture not the monetary value. 

[![Five yen at shrine][1]][1]

The Japanese for “five yen,” go en (五円) is a homophone with go-en (御縁), “en” being a word for causal connection or relationship, and “go” being a respectful prefix. As a result, five-yen coins are commonly given as donations at Shinto shrines with the intention of establishing a good connection with the deity of the shrine, and is widely believed it is best to insert a single five-yen coin into a new wallet before inserting any other money.

The reason why the five yen coin is lucky is because it’s called a “go-EN” coin. The number 5 is “go” in Japanese, and “yen” is pronounced more like “en.”

To be precise, “go-EN” means “honorably good luck” especially in terms of relationships. So people throw in these coins at a temple hoping to meet new people who might bring fortune, business, friendship or love.

Source: [tokiotours][1] 


  [1]: https://tokiotours.wordpress.com/2013/07/12/significance-of-the-5-yen-coin/