Table 3. Monovalent cation binding in crystal structures of P-loop NTPases.
Protein | PDB entry | Bound NTP analog | Occupation of the AG site | Phosphate chain shape | |||
---|---|---|---|---|---|---|---|
Cation | Distance to the closest O atom of PA, Å* | Distance to the closest O atom of PG, Å*,† | PA-PG distance, Å* | PB-O3B-PG angle, degrees† | |||
TRAFAC class NTPases | |||||||
GTPase MnmE(TrmE) | 2gj8 | GDP AlF4- | K+ | 2.8 | 2.6 | 5.4 | 136.3 |
2gja | GDP AlF4- | NH4+ | 2.9 | 2.5 | 5.4 | 136.9 | |
2gj9 | GDP AlF4- | Rb+ | 2.9 | 2.8 | 5.5 | 131.6 | |
GTPase FeoB | 3ss8 | GDP AlF4- | K+ | 2.8 | 2.6 | 5.4 | 144.9 |
Dynamin-like proteins | 2x2e | GDP AlF4- | Na+ | 4.0 | 2.5 | 5.3 | 131.2 |
2x2f | GDP AlF4- | Na+ | 4.1 | 2.6 | 5.3 | 133.6 | |
3w6p | GDP AlF4- | Na+ | 4 | 2.4 | 5.5 | 135.3 | |
3t34 | GDP AlF4- | Na+ | 3.8 | 2.4 | 5.6 | 149.3 | |
GTPase Era | 3r9w | GNP | H2O‡ | 3 | 3.4 | 5.1 | 129.2 |
Eukaryotic translation initiation factor eIF5B | 4ncn | GTP | Na+ | 2.4 | 2.4 | 5.0 | 126.6 |
4tmv | GSP | Na+ | 2.4 | 2.8 (S)§ | 4.9 | 126.3 | |
4tmw | GTP | Na+ | 2.4 | 2.4 | 4.9 | 125.9 | |
4tmz | GSP | K+ | 2.7 | 3.3 (S)§ | 4.9 | 122.1 | |
RecA/F1-like class NTPases | |||||||
DNA recombinase RadA | 3ew9 | ANP | K+ | 6.2 | 3.3 | 5.1 | 124.5 |
2f1h | ANP | K+ | 6.6 | 3.5 | 5.3 | 125.3 | |
2fpm | ANP | K+ | 5.9 | 2.6 | 5.1 | 124.2 | |
1xu4 | ANP | K+ | 6.1 | 2.7 | 5.2 | 125.0 |
*The values were measured directly in the respective protein structures displayed in PyMOL.
† If the γ-phosphate was replaced by an AlF4- complex, the distance was measured to the closest F atom.
‡ While GTPase Era has been shown to be K+-dependent (Rafay et al., 2012; Meier et al., 2000), the crystallization solution contained no K+, only Na+, so that the likely cation-binding site is occupied by a water molecule, which forms hydrogen bonds with K+ ligands.
§ Non-hydrolyzable GTP analog GDP-monothiophosphate (GSP) contains a sulfur atom in the place of the O1G atom of γ-phosphate; this atom in involved in coordination of monovalent cations in respective structures.