. 2018 Dec 11;7:e37373. doi: 10.7554/eLife.37373

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
Protein	PDB entry	Bound NTP analog	Cation	Distance to the closest O atom of P^A, Å^*	Distance to the closest O atom of P^G, Å^*,†	P^A-P^G distance, Å^*	P^B-O^3B-P^G 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 O^1G atom of γ-phosphate; this atom in involved in coordination of monovalent cations in respective structures.