Figure 1. Mg-NTP complexes and their binding in the active sites of P-loop NTPases.

Phosphate chains of NTP molecules and their analogs are colored by atoms: oxygen atoms in red, phosphorus in orange. The K⁺ ion is shown as a purple sphere, Na⁺ ion is shown as a blue sphere, Mg²⁺ ions are shown as green spheres. Phosphate chain is shown in stick representation with oxygens in red and phosphorus atoms in orange; γ-phosphate mimicking groups (AlF₄^- and MgF_3^-) are shown in black, coordination and hydrogen bonds are shown as black dashed lines. (A) Active site of the small Ras-like GTPase RhoA in complex with the activating protein RhoGAP [PDB entry 1OW3]; the bound GDP-MgF_3^- mimics the transition state. The P-loop with the preceding α-helix is shown as green cartoon; Switch I motif with the conserved Mg²⁺-binding Thr residue is shown in magenta; Switch II motif (DxxG motif, which starts from the conserved Asp of the Walker B motif) is shown in orange; the Arg finger of RhoGAP is colored turquoise. (B) Active site of the K⁺-dependent GTPase MnmE with bound GDP-AlF₄^- [PDB: 2GJ8]. Switch I region and the K-loop are shown in magenta. (C) The active site of dynamin, a Na⁺-adapted GTPase with bound GDP-AlF₄^- [PDB: 2X2E]. The P-loop and K-loop (Switch I region) are colored as in panels A and B. (D) Structure of the NTP triphosphate chain with Mg²⁺ ion in a bidentate coordination, referred to as the βγ conformation. The pink dotted arch indicates the P^B-O^3B-P^G angle; the blue dashed line indicates the P^A-P^G distance. The atom names are in accordance with the CHARMM naming scheme (Vanommeslaeghe et al., 2010) and the recent IUPAC recommendations (Blackburn et al., 2017).