The 'arm' designation originates from the time when only the secondary structure was known ('cloverleaf') and is somewhat misleading in the tertiary structure  .

The structures marked red and dark green in the left frame are magnesium ions partly coordinated with water molecules. They stabilize the tRNA once it is folded to its final form. One magnesium in the variable loop is completely (tetrahedrally) coordinated with water (shown as red spheres here)  . The waters are hydrogen bridged to the phosphate backbone of U8 to U12  . Another magnesium surrounded by six waters is situated in the anticodon arm and held by G24, C25 and 5MC40 - G42  . Some more tightly bound water molecules are involved in hydrogen bridges  . Other magnesiums are partly coordinated to the backbone phosphate groups

The backbone of the tRNA is partly stabilized by water molecules as shown here for the T psi C arm (G51 - U59)  . The water molecules bind to posphate oxygens to bridge two nucleotides each  .
Some twin water molecules bridge the ribose 2' hydroxyl group to a phosphate oxygen of the next nucleotide  .

The most rigid part of the tRNA is the central domain formed by the D arm and the T psi C arm (which are folded tightly together) as judged from the temperature factor of the X-ray data (blue = rigid, red = movable).