load matrix
[N,C]=hist3([longitude, latitude],[50 50]);
figure
hist3([longitude, latitude],[50 50],'CDataMode','auto')
view(2)
% the distance between this point and the centers
% of the non-zero bins will be calculated:
P = [-17 34];
[x,y] = ndgrid(C{:});
idx = N > 0;
d = sqrt((x(idx)-P(1)).^2 + (y(idx)-P(2)).^2)
Note that that's Euclidean distance (in degrees lat/lon); the actual distance along the surface of the earth will be different (since the earth is not in fact flat), and if you need that you can use the Haversine formula, code for which can be found on the File Exchange.
