The GDP is located in a shallow pocket on the surface of Ran protein and was bound through interactions in its heterocyclic ring, sugar and phosphate groups as well as to a Mg²⁺ that is bound to Thr24 and to Asp65, Thr66 and Glu70 via water molecules.

Click to see the detail of the area surrounding the GDP, Ran and NTF2

Water247 is bound to both the Mg²⁺ and to Asp94 of NTF2. Although it is located adjacent to the NTF2-Ran interface, GDP is not buried by the interaction (for more details on the binding of GDP to Ran, see ref. 7).