Coordinates and distances are independent concepts. They are function from the space you are working with into the reals assigning each respectively each pair of elements a real number for each coordinate respectively one real number for the distance. You can for various reasons choose coordinates and distances in a way such that they have simple mathematical relationships but that is just an arbitrary choice. The classical law of gravity is only dependent on distances, which is a physical meaningful concept, but not on coordinates, which are not physically meaningful. In that sense distances are fundamental in a way in which coordinates are not and a distance of zero is a meaningful thing, namely two things are at the very same place.