I would rearrange your code to set everythign up before entering the for loop, and then in the loop, just update the plot data. It might look something like this (untested)
figure;
figure;
s1 = scatter3(nan,nan,nan, 'b', 'filled');
hold on;
s2 = scatter3(nan,nan,nan, 'k', 'filled');
hold off;
xlabel('x [mm]')
ylabel('y [mm]')
zlabel('z [mm]')
legend('STB','7DOF Fit')
view(3)
set(gcf, 'Color', 'White');
set(gca, 'Fontsize', 12);
grid on; grid minor;
axis equal;
set(gca, 'ZDir','reverse');
for i=1:numel(Coordinates(:,1))
title(['Time = ', num2str(round(DD{i}(1,1),2)), ' s'])
s1.XData = DD{i}(:,2);
s1.YData = DD{i}(:,3);
s1.ZData = DD{i}(:,4);
s2.XData = Coordinates{i,1};
s2.YData = Coordinates{i,2};
s2.ZData = Coordinates{i,3};
drawnow;
pause(0.001);
end
