Sodium in PDB 4tmx: Translation Initiation Factor EIF5B (517-858) Mutant D533N From C. Thermophilum, Bound to Gtp and Sodium

The structure of Translation Initiation Factor EIF5B (517-858) Mutant D533N From C. Thermophilum, Bound to Gtp and Sodium, PDB code: 4tmx was solved by B.Kuhle, F.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.43 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.530, 116.820, 66.490, 90.00, 101.02, 90.00
R / Rfree (%)	15.5 / 18.2

The structure of Translation Initiation Factor EIF5B (517-858) Mutant D533N From C. Thermophilum, Bound to Gtp and Sodium also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Translation Initiation Factor EIF5B (517-858) Mutant D533N From C. Thermophilum, Bound to Gtp and Sodium (pdb code 4tmx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Translation Initiation Factor EIF5B (517-858) Mutant D533N From C. Thermophilum, Bound to Gtp and Sodium, PDB code: 4tmx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Translation Initiation Factor EIF5B (517-858) Mutant D533N From C. Thermophilum, Bound to Gtp and Sodium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Translation Initiation Factor EIF5B (517-858) Mutant D533N From C. Thermophilum, Bound to Gtp and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:15.3 occ:1.00 O A:GLY555 2.3 17.1 1.0 OD1 A:ASN533 2.3 16.3 1.0 O1A A:GTP901 2.3 13.9 1.0 O1G A:GTP901 2.4 14.8 1.0 O3B A:GTP901 2.4 12.3 1.0 PG A:GTP901 3.0 13.1 1.0 O A:HOH1086 3.1 14.2 1.0 C A:GLY555 3.4 15.4 1.0 CG A:ASN533 3.5 14.6 1.0 PA A:GTP901 3.5 13.4 1.0 CA A:ILE556 3.5 16.1 1.0 O3A A:GTP901 3.5 12.8 1.0 PB A:GTP901 3.6 12.7 1.0 CG2 A:ILE556 3.9 17.4 1.0 O3G A:GTP901 3.9 12.6 1.0 N A:ILE556 3.9 15.3 1.0 C5' A:GTP901 4.0 16.1 1.0 CA A:ASN533 4.0 12.1 1.0 O1B A:GTP901 4.1 11.6 1.0 N A:ASN533 4.2 12.7 1.0 CB A:ILE556 4.2 20.6 1.0 O2G A:GTP901 4.2 13.0 1.0 O5' A:GTP901 4.3 13.7 1.0 O A:HOH1210 4.3 37.8 1.0 NE2 A:GLN549 4.3 16.1 1.0 CB A:ASN533 4.3 14.1 1.0 ND2 A:ASN533 4.3 19.5 1.0 N A:THR557 4.4 13.2 1.0 O A:HOH1182 4.4 29.9 1.0 MG A:MG903 4.5 12.9 1.0 C A:ILE556 4.5 16.9 1.0 OE1 A:GLU552 4.6 17.8 1.0 CA A:GLY555 4.6 15.7 1.0 O2A A:GTP901 4.7 12.9 1.0 O2B A:GTP901 4.8 11.9 1.0 CG2 A:VAL532 4.9 16.1 1.0

Sodium binding site 2 out of 2 in the Translation Initiation Factor EIF5B (517-858) Mutant D533N From C. Thermophilum, Bound to Gtp and Sodium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Translation Initiation Factor EIF5B (517-858) Mutant D533N From C. Thermophilum, Bound to Gtp and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:13.8 occ:1.00 O B:GLY555 2.2 15.5 1.0 OD1 B:ASN533 2.2 15.4 1.0 O1G B:GTP901 2.4 12.9 1.0 O3B B:GTP901 2.4 11.7 1.0 O1A B:GTP901 2.4 12.4 1.0 O B:HOH1089 3.0 13.3 1.0 PG B:GTP901 3.0 12.2 1.0 C B:GLY555 3.4 16.4 1.0 CG B:ASN533 3.4 13.6 1.0 CA B:ILE556 3.5 13.3 0.3 PA B:GTP901 3.6 12.2 1.0 O3A B:GTP901 3.6 12.1 1.0 PB B:GTP901 3.6 11.7 1.0 CA B:ILE556 3.8 15.1 0.7 CG2 B:ILE556 3.9 15.5 0.3 O3G B:GTP901 3.9 12.2 1.0 N B:ILE556 3.9 14.6 0.3 N B:ILE556 4.0 14.5 0.7 CA B:ASN533 4.0 12.8 1.0 C5' B:GTP901 4.1 13.4 1.0 O2B B:GTP901 4.1 11.3 1.0 O B:HOH1027 4.2 21.9 1.0 O2G B:GTP901 4.2 12.4 1.0 N B:ASN533 4.2 13.5 1.0 CB B:ILE556 4.2 13.7 0.3 N B:THR557 4.3 12.2 1.0 CD1 B:ILE556 4.3 17.9 0.7 CB B:ASN533 4.3 14.1 1.0 ND2 B:ASN533 4.3 16.1 1.0 O5' B:GTP901 4.4 13.0 1.0 MG B:MG903 4.4 12.1 1.0 NE2 B:GLN549 4.4 15.8 1.0 C B:ILE556 4.4 14.7 0.3 O B:HOH1074 4.5 36.6 1.0 C B:ILE556 4.5 12.9 0.7 OE1 B:GLU552 4.5 17.2 1.0 CA B:GLY555 4.6 15.1 1.0 O1B B:GTP901 4.8 11.5 1.0 O2A B:GTP901 4.8 12.5 1.0 CG1 B:ILE556 5.0 15.9 0.7 CB B:ILE556 5.0 15.8 0.7 CG2 B:VAL532 5.0 13.2 1.0

B.Kuhle, R.Ficner. A Monovalent Cation Acts As Structural and Catalytic Cofactor in Translational Gtpases. Embo J. 2014.
ISSN: ESSN 1460-2075
PubMed: 25225612
DOI: 10.15252/EMBJ.201488517