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

The structure of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtp and Sodium, PDB code: 4tmw 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)	43.37 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.610, 116.450, 66.240, 90.00, 101.15, 90.00
R / Rfree (%)	15.7 / 18.4

The structure of Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtp 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 Gtp and Sodium (pdb code 4tmw). 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 Gtp and Sodium, PDB code: 4tmw:
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 Gtp 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 Gtp and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:13.4 occ:1.00 O1G A:GTP901 1.9 11.8 1.0 OG1 A:THR557 2.0 14.4 1.0 O A:HOH1060 2.1 12.0 1.0 O A:HOH1061 2.1 13.7 1.0 O2B A:GTP901 2.1 12.3 1.0 OG1 A:THR537 2.2 13.2 1.0 CB A:THR557 3.0 12.6 1.0 PG A:GTP901 3.1 13.0 1.0 CB A:THR537 3.2 11.6 1.0 PB A:GTP901 3.3 13.0 1.0 O3B A:GTP901 3.4 12.2 1.0 N A:THR537 3.8 11.4 1.0 N A:THR557 3.9 12.5 1.0 O3G A:GTP901 3.9 15.7 1.0 CA A:THR557 4.0 12.3 1.0 OE2 A:GLU552 4.1 15.1 1.0 CG2 A:THR557 4.1 15.3 1.0 CA A:THR537 4.1 10.2 1.0 OD2 A:ASP594 4.2 15.1 1.0 O1A A:GTP901 4.2 15.3 1.0 OE1 A:GLU552 4.2 16.7 1.0 CG2 A:THR537 4.3 12.9 1.0 O2G A:GTP901 4.3 12.7 1.0 O1B A:GTP901 4.3 13.1 1.0 OD1 A:ASP594 4.4 14.6 1.0 O3A A:GTP901 4.4 12.4 1.0 O A:THR595 4.5 14.1 1.0 NA A:NA902 4.5 15.9 1.0 CE A:LYS536 4.5 13.4 1.0 CD A:GLU552 4.6 15.3 1.0 PA A:GTP901 4.6 14.0 1.0 O2A A:GTP901 4.7 13.6 1.0 CG A:ASP594 4.7 13.4 1.0 NH2 A:ARG806 4.7 25.2 1.0 CB A:LYS536 4.8 12.1 1.0 C A:ILE556 4.9 15.4 1.0 C A:LYS536 4.9 10.1 1.0

Magnesium binding site 2 out of 2 in the Translation Initiation Factor EIF5B (517-858) From C. Thermophilum, Bound to Gtp 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 Gtp and Sodium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:12.9 occ:1.00 O1G B:GTP901 1.9 12.8 1.0 O2B B:GTP901 2.1 12.3 1.0 O B:HOH1060 2.1 12.3 1.0 OG1 B:THR557 2.1 13.3 1.0 O B:HOH1059 2.2 13.2 1.0 OG1 B:THR537 2.2 12.6 1.0 CB B:THR557 3.1 12.9 1.0 PG B:GTP901 3.1 12.8 1.0 CB B:THR537 3.2 11.5 1.0 PB B:GTP901 3.2 13.1 1.0 O3B B:GTP901 3.3 13.4 1.0 N B:THR537 3.8 12.1 1.0 O3G B:GTP901 3.9 13.7 1.0 N B:THR557 4.0 12.6 1.0 CA B:THR537 4.1 12.1 1.0 CG2 B:THR557 4.1 13.1 1.0 CA B:THR557 4.1 13.8 1.0 OE2 B:GLU552 4.2 15.0 1.0 O1B B:GTP901 4.2 12.4 1.0 O1A B:GTP901 4.2 14.2 1.0 OE1 B:GLU552 4.2 16.1 1.0 OD2 B:ASP594 4.3 15.0 1.0 O2G B:GTP901 4.3 12.4 1.0 CG2 B:THR537 4.3 13.7 1.0 OD1 B:ASP594 4.3 12.4 1.0 O3A B:GTP901 4.3 13.9 1.0 CE B:LYS536 4.4 12.3 1.0 O B:THR595 4.4 13.3 1.0 NA B:NA902 4.4 15.5 1.0 PA B:GTP901 4.6 13.0 1.0 O2A B:GTP901 4.7 13.9 1.0 CD B:GLU552 4.7 17.2 1.0 CG B:ASP594 4.7 13.5 1.0 CB B:LYS536 4.7 11.2 1.0 NH2 B:ARG806 4.8 17.0 1.0 C B:LYS536 4.9 13.0 1.0 NZ B:LYS536 4.9 12.0 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