Sodium in PDB 4tmv: Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Sodium

The structure of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Sodium, PDB code: 4tmv 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)	43.19 / 1.53
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.640, 115.850, 66.090, 90.00, 101.35, 90.00
R / Rfree (%)	16.3 / 18.8

The structure of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas 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) From C. Thermophilum, Bound to Gtpgammas and Sodium (pdb code 4tmv). 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) From C. Thermophilum, Bound to Gtpgammas and Sodium, PDB code: 4tmv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas 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) From C. Thermophilum, Bound to Gtpgammas and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ B:Na903 b:21.3 occ:1.00 O B:GLY555 2.3 18.9 1.0 OD2 B:ASP533 2.4 25.3 1.0 O1A B:GSP901 2.4 16.4 1.0 O3B B:GSP901 2.6 15.3 1.0 S1G B:GSP901 2.8 18.4 1.0 PG B:GSP901 3.3 14.6 1.0 O B:HOH1074 3.3 15.7 1.0 C B:GLY555 3.5 23.1 1.0 PA B:GSP901 3.5 15.8 1.0 O3A B:GSP901 3.6 14.6 1.0 CG B:ASP533 3.6 29.5 1.0 O B:HOH1325 3.7 42.4 1.0 PB B:GSP901 3.7 15.2 1.0 C5' B:GSP901 3.9 17.8 1.0 O2G B:GSP901 4.0 17.1 1.0 CA B:ASP533 4.1 17.8 1.0 CA B:ILE556 4.2 16.6 1.0 NE2 B:GLN549 4.2 21.5 1.0 O2B B:GSP901 4.2 13.4 1.0 O5' B:GSP901 4.2 15.9 1.0 N B:ILE556 4.3 20.4 1.0 N B:ASP533 4.3 17.7 1.0 OD1 B:ASP533 4.4 36.8 1.0 CB B:ASP533 4.5 27.4 1.0 CD1 B:ILE556 4.5 23.9 1.0 MG B:MG902 4.5 14.9 1.0 CA B:GLY555 4.5 21.9 1.0 O3G B:GSP901 4.6 15.1 1.0 O2A B:GSP901 4.8 15.7 1.0 N B:THR557 4.8 14.5 1.0 OE1 B:GLU552 4.8 19.1 1.0 O1B B:GSP901 5.0 15.9 1.0 C B:ILE556 5.0 15.1 1.0

Sodium binding site 2 out of 2 in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas 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) From C. Thermophilum, Bound to Gtpgammas and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:19.3 occ:1.00 O A:GLY555 2.2 22.9 1.0 OD2 A:ASP533 2.3 22.3 1.0 O2A A:GSP901 2.4 18.5 1.0 O3B A:GSP901 2.7 16.8 1.0 S1G A:GSP901 2.9 19.4 1.0 PG A:GSP901 3.3 15.7 1.0 O A:HOH1015 3.4 44.1 1.0 C A:GLY555 3.4 23.0 1.0 CG A:ASP533 3.5 24.2 1.0 PA A:GSP901 3.5 16.7 1.0 O3A A:GSP901 3.6 15.1 1.0 O A:HOH1057 3.6 17.1 1.0 PB A:GSP901 3.8 15.9 1.0 C5' A:GSP901 3.9 16.9 1.0 O3G A:GSP901 3.9 18.1 1.0 CA A:ASP533 4.0 18.0 1.0 CA A:ILE556 4.1 19.3 1.0 N A:ASP533 4.1 18.5 1.0 CD1 A:ILE556 4.2 37.2 1.0 N A:ILE556 4.2 18.3 1.0 O5' A:GSP901 4.2 16.0 1.0 NE2 A:GLN549 4.2 21.9 1.0 O2B A:GSP901 4.3 15.1 1.0 CB A:ASP533 4.3 18.7 1.0 OD1 A:ASP533 4.4 26.7 1.0 CA A:GLY555 4.4 24.8 1.0 MG A:MG902 4.7 15.7 1.0 O2G A:GSP901 4.8 16.7 1.0 O1A A:GSP901 4.8 17.0 1.0 CG1 A:ILE556 4.9 25.7 1.0 CG2 A:VAL532 4.9 22.0 0.3 N A:THR557 4.9 15.9 1.0 CG1 A:VAL532 5.0 20.3 0.7 O1B A:GSP901 5.0 15.0 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