The Wolverine filmed at Tomonoura, Fukuyama. This fishing harbour, which the film presents as a town near Nagasaki, is the place Logan and Yukio reach. On screen it's Nagasaki suburb.
Probable Named in published production coverage; the coordinate is the place itself, checked against a gazetteer. This is an area, not a spot. The coordinate is its middle, so use it to navigate to the place and not to line up a shot.
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Venture keeps every scene location on one map, sorted by how far you'd have to walk. Open it in Fukuyama and it tells you what was shot around you, how to get there, and whether you can actually go in.
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