Magnesium in PDB 5mi3: Structure of Phosphorylated Translation Elongation Factor Ef-Tu From E. Coli

The structure of Structure of Phosphorylated Translation Elongation Factor Ef-Tu From E. Coli, PDB code: 5mi3 was solved by A.Talavera, J.Hendrix, W.Versees, S.De Gieter, D.Castro-Roa, D.Jurenas, K.Van Nerom, N.Vandenberk, A.Barth, H.De Greve, J.Hofkens, N.Zenkin, R.Loris, A.Garcia-Pino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.77 / 2.80
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.200, 244.400, 61.740, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 19.8

The binding sites of Magnesium atom in the Structure of Phosphorylated Translation Elongation Factor Ef-Tu From E. Coli (pdb code 5mi3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Phosphorylated Translation Elongation Factor Ef-Tu From E. Coli, PDB code: 5mi3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Phosphorylated Translation Elongation Factor Ef-Tu From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Phosphorylated Translation Elongation Factor Ef-Tu From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:20.3 occ:1.00 O A:HOH516 1.8 15.1 1.0 O A:HOH543 1.8 13.9 1.0 O A:HOH530 1.9 20.5 1.0 O3B A:GDP402 2.0 18.1 1.0 OG1 A:THR26 2.2 15.1 1.0 O A:HOH546 2.3 13.3 1.0 CB A:THR26 3.2 15.5 1.0 PB A:GDP402 3.2 25.2 1.0 O1B A:GDP402 3.3 17.6 1.0 N A:THR26 3.8 13.6 1.0 O1A A:GDP402 4.0 21.1 1.0 OD1 A:ASP51 4.0 31.9 1.0 CA A:THR26 4.1 14.4 1.0 O A:CYS82 4.2 23.6 1.0 OD2 A:ASP81 4.2 22.9 1.0 O2B A:GDP402 4.2 21.2 1.0 O3A A:GDP402 4.2 19.9 1.0 CG2 A:THR26 4.2 16.7 1.0 O A:PRO83 4.3 26.1 1.0 PA A:GDP402 4.4 13.6 1.0 O2A A:GDP402 4.5 18.2 1.0 CA A:PRO83 4.5 25.1 1.0 O A:HOH536 4.5 21.5 1.0 O A:HOH508 4.6 38.6 1.0 OD1 A:ASP81 4.7 25.9 1.0 CG A:ASP81 4.9 23.0 1.0 C A:CYS82 4.9 20.8 1.0 C A:PRO83 4.9 25.4 1.0 CB A:LYS25 4.9 11.6 1.0 C A:LYS25 5.0 17.1 1.0 CG A:ASP51 5.0 32.9 1.0

Magnesium binding site 2 out of 2 in the Structure of Phosphorylated Translation Elongation Factor Ef-Tu From E. Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Phosphorylated Translation Elongation Factor Ef-Tu From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:20.1 occ:1.00 OG1 B:THR26 1.9 46.2 1.0 O B:HOH533 2.0 20.6 1.0 O3B B:GDP402 2.1 35.8 1.0 O B:HOH510 2.1 23.2 1.0 O B:HOH509 2.1 15.3 1.0 O B:HOH506 2.2 14.5 1.0 CB B:THR26 3.0 31.2 1.0 PB B:GDP402 3.2 32.8 1.0 O2B B:GDP402 3.4 37.5 1.0 N B:THR26 3.8 37.3 1.0 OD2 B:ASP81 3.9 46.4 1.0 O2A B:GDP402 3.9 35.1 1.0 CA B:THR26 4.0 36.3 1.0 CG2 B:THR26 4.0 31.2 1.0 O B:HOH527 4.0 22.1 1.0 O B:CYS82 4.1 38.7 1.0 OD1 B:ASP51 4.1 41.8 1.0 O1B B:GDP402 4.1 31.5 1.0 CA B:PRO83 4.4 42.8 1.0 O3A B:GDP402 4.4 25.8 1.0 O B:PRO83 4.4 48.1 1.0 OD1 B:ASP81 4.5 52.6 1.0 PA B:GDP402 4.5 31.0 1.0 O1A B:GDP402 4.6 32.4 1.0 CG B:ASP81 4.6 46.2 1.0 C B:CYS82 4.8 39.0 1.0 C B:PRO83 4.9 44.6 1.0 C B:LYS25 4.9 38.5 1.0 N B:PRO83 5.0 41.8 1.0 CB B:LYS25 5.0 30.4 1.0

A.Talavera, J.Hendrix, W.Versees, D.Jurenas, K.Van Nerom, N.Vandenberk, R.K.Singh, A.Konijnenberg, S.De Gieter, D.Castro-Roa, A.Barth, H.De Greve, F.Sobott, J.Hofkens, N.Zenkin, R.Loris, A.Garcia-Pino. Phosphorylation Decelerates Conformational Dynamics in Bacterial Translation Elongation Factors. Sci Adv V. 4 P9714 2018.
ISSN: ESSN 2375-2548
PubMed: 29546243
DOI: 10.1126/SCIADV.AAP9714