We report significant anisotropies in the projected two-dimensional (2D) spatial distributions of Globular Clusters (GCs) of the giant Virgo elliptical galaxy NGC4649 (M60). Similar features are found in the 2D distribution of low-mass X-ray binaries (LMXBs), both associated with GCs and in the stellar field. Deviations from azimuthal symmetry suggest an arc-like excess of GCs extending north at 4-15 kpc galactocentric radii in the eastern side of major axis of NGC4649. This feature is more prominent for red GCs, but still persists in the 2D distribution of blue GCs. High and low luminosity GCs also show some segregation along this arc, with high-luminosity GCs preferentially located in the southern end and low-luminosity GCs in the northern section of the arc. GC-LMXBs follow the anisotropy of red-GCs, where most of them reside; however, a significant overdensity of (high-luminosity) field LMXBs is present to the south of the GC arc. These results suggest that NGC4649 has experienced mergers and/or multiple accretions of less massive satellite galaxies during its evolution, of which the GCs in the arc may be the fossil remnant. We speculate that the observed anisotropy in the field LMXB spatial distribution indicates that these X-ray binaries may be the remnants of a star formation event connected with the merger, or maybe be ejected from the parent red GCs, if the bulk motion of these clusters is significantly affected by dynamical friction. We also detect a luminosity enhancement in the X-ray source population of the companion spiral galaxy NGC4647. We suggest that these may be younger high mass X-ray binaries formed as a result of the tidal interaction of this galaxy with NGC4649.