Magnesium in PDB 4tn1: Translation Initiation Factor EIF5B (517-858) Mutant D533R From C. Thermophilum, Bound to Gtpgammas

The structure of Translation Initiation Factor EIF5B (517-858) Mutant D533R From C. Thermophilum, Bound to Gtpgammas, PDB code: 4tn1 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)	47.50 / 2.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	115.690, 115.690, 119.800, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.7

The binding sites of Magnesium atom in the Translation Initiation Factor EIF5B (517-858) Mutant D533R From C. Thermophilum, Bound to Gtpgammas (pdb code 4tn1). 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) Mutant D533R From C. Thermophilum, Bound to Gtpgammas, PDB code: 4tn1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Translation Initiation Factor EIF5B (517-858) Mutant D533R From C. Thermophilum, Bound to Gtpgammas


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) Mutant D533R From C. Thermophilum, Bound to Gtpgammas within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:43.4 occ:1.00 O2B B:GSP901 1.9 41.7 1.0 O3G B:GSP901 1.9 26.9 1.0 OG1 B:THR537 1.9 44.6 1.0 O B:HOH1030 2.0 68.9 1.0 O B:HOH1029 2.2 72.1 1.0 OG1 B:THR557 2.3 33.8 1.0 PB B:GSP901 3.1 35.8 1.0 CB B:THR537 3.2 43.5 1.0 PG B:GSP901 3.2 52.5 1.0 CB B:THR557 3.3 35.5 1.0 O3B B:GSP901 3.5 25.4 1.0 N B:THR537 3.7 36.0 1.0 O1B B:GSP901 4.0 39.0 1.0 CA B:THR537 4.0 36.1 1.0 CG2 B:THR557 4.1 27.0 1.0 O2A B:GSP901 4.1 37.1 1.0 S1G B:GSP901 4.2 43.2 1.0 OE2 B:GLU552 4.2 53.0 1.0 CG2 B:THR537 4.2 30.1 1.0 CE B:LYS536 4.3 31.1 1.0 OD2 B:ASP594 4.3 40.1 1.0 O2G B:GSP901 4.3 38.5 1.0 O3A B:GSP901 4.3 49.4 1.0 CB B:LYS536 4.4 28.5 1.0 OD1 B:ASP594 4.5 61.7 1.0 OE1 B:GLU552 4.5 31.9 1.0 CA B:THR557 4.5 41.0 1.0 PA B:GSP901 4.5 50.4 1.0 N B:THR557 4.6 38.2 1.0 O B:THR595 4.6 26.3 1.0 O1A B:GSP901 4.6 34.5 1.0 NZ B:LYS536 4.7 27.4 1.0 CG B:ASP594 4.7 46.2 1.0 C B:LYS536 4.8 41.0 1.0 CD B:GLU552 4.8 47.5 1.0 CA B:LYS536 5.0 36.5 1.0

Magnesium binding site 2 out of 2 in the Translation Initiation Factor EIF5B (517-858) Mutant D533R From C. Thermophilum, Bound to Gtpgammas


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) Mutant D533R From C. Thermophilum, Bound to Gtpgammas within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:59.0 occ:1.00 O3G A:GSP901 1.9 34.4 1.0 OG1 A:THR537 1.9 63.0 1.0 OG1 A:THR557 2.0 42.5 1.0 O A:HOH1015 2.1 56.3 1.0 O2B A:GSP901 2.2 41.5 1.0 O A:HOH1016 2.2 60.7 1.0 CB A:THR557 3.1 42.7 1.0 CB A:THR537 3.2 60.1 1.0 PG A:GSP901 3.2 47.0 1.0 PB A:GSP901 3.3 48.7 1.0 O3B A:GSP901 3.4 48.2 1.0 OE2 A:GLU552 3.9 67.7 1.0 N A:THR537 3.9 51.2 1.0 CG2 A:THR557 4.0 34.4 1.0 O2A A:GSP901 4.1 57.7 1.0 OE1 A:GLU552 4.1 62.1 1.0 CA A:THR537 4.1 52.2 1.0 CG2 A:THR537 4.1 56.6 1.0 OD2 A:ASP594 4.1 50.1 1.0 S1G A:GSP901 4.2 54.2 1.0 O2G A:GSP901 4.2 44.6 1.0 O1B A:GSP901 4.2 52.0 1.0 CA A:THR557 4.2 47.4 1.0 N A:THR557 4.3 46.0 1.0 O3A A:GSP901 4.4 54.9 1.0 CD A:GLU552 4.4 61.2 1.0 OD1 A:ASP594 4.5 56.4 1.0 CE A:LYS536 4.5 37.7 1.0 PA A:GSP901 4.6 51.5 1.0 O1A A:GSP901 4.6 45.7 1.0 O A:THR595 4.7 40.9 1.0 CG A:ASP594 4.7 56.7 1.0 CB A:LYS536 4.7 45.7 1.0 NZ A:LYS536 4.8 38.5 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