Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtpgammas and Sodium, PDB code: 4tmv:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg902 b:14.9 occ:1.00 O2G B:GSP901 2.0 17.1 1.0 O2B B:GSP901 2.0 13.4 1.0 OG1 B:THR557 2.1 14.4 1.0 O B:HOH1075 2.1 15.2 1.0 O B:HOH1074 2.1 15.7 1.0 OG1 B:THR537 2.2 14.2 1.0 CB B:THR557 3.1 14.0 1.0 CB B:THR537 3.2 12.5 1.0 PB B:GSP901 3.2 15.2 1.0 PG B:GSP901 3.2 14.6 1.0 O3B B:GSP901 3.4 15.3 1.0 N B:THR537 3.9 13.9 1.0 CG2 B:THR557 4.1 14.8 1.0 N B:THR557 4.1 14.5 1.0 CA B:THR537 4.1 13.5 1.0 CA B:THR557 4.2 14.3 1.0 OE1 B:GLU552 4.2 19.1 1.0 OE2 B:GLU552 4.2 16.4 1.0 O1A B:GSP901 4.2 16.4 1.0 O1B B:GSP901 4.2 15.9 1.0 OD2 B:ASP594 4.2 14.6 1.0 O3G B:GSP901 4.3 15.1 1.0 CG2 B:THR537 4.3 15.7 1.0 O3A B:GSP901 4.3 14.6 1.0 OD1 B:ASP594 4.4 14.7 1.0 NA B:NA903 4.5 21.3 1.0 PA B:GSP901 4.6 15.8 1.0 S1G B:GSP901 4.6 18.4 1.0 O2A B:GSP901 4.6 15.7 1.0 O B:THR595 4.6 15.4 1.0 CD B:GLU552 4.6 18.6 1.0 CE B:LYS536 4.6 14.2 1.0 CG B:ASP594 4.7 13.3 1.0 NH2 B:ARG806 4.8 21.6 1.0 CB B:LYS536 4.9 14.0 1.0 C B:LYS536 5.0 15.6 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg902 b:15.7 occ:1.00 O3G A:GSP901 2.0 18.1 1.0 O A:HOH1058 2.0 15.3 1.0 O2B A:GSP901 2.1 15.1 1.0 OG1 A:THR557 2.1 15.2 1.0 OG1 A:THR537 2.1 14.2 1.0 O A:HOH1057 2.1 17.1 1.0 CB A:THR557 3.1 16.7 1.0 CB A:THR537 3.1 14.8 1.0 PG A:GSP901 3.3 15.7 1.0 PB A:GSP901 3.3 15.9 1.0 O3B A:GSP901 3.5 16.8 1.0 N A:THR537 3.9 13.2 1.0 N A:THR557 4.1 15.9 1.0 CA A:THR537 4.1 13.7 1.0 CG2 A:THR557 4.1 17.7 1.0 O2G A:GSP901 4.1 16.7 1.0 CA A:THR557 4.1 16.9 1.0 OD2 A:ASP594 4.2 17.0 1.0 OE2 A:GLU552 4.2 17.9 1.0 CG2 A:THR537 4.2 16.6 1.0 O2A A:GSP901 4.2 18.5 1.0 OE1 A:GLU552 4.2 18.0 1.0 OD1 A:ASP594 4.3 15.4 1.0 O1B A:GSP901 4.3 15.0 1.0 O3A A:GSP901 4.4 15.1 1.0 PA A:GSP901 4.5 16.7 1.0 O1A A:GSP901 4.5 17.0 1.0 O A:THR595 4.6 17.0 1.0 CG A:ASP594 4.6 15.4 1.0 CD A:GLU552 4.6 16.8 1.0 CE A:LYS536 4.7 16.6 1.0 NA A:NA903 4.7 19.3 1.0 S1G A:GSP901 4.8 19.4 1.0 NH2 A:ARG806 4.8 25.1 1.0 CB A:LYS536 4.9 12.8 1.0 C A:LYS536 5.0 14.5 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