Magnesium in PDB 5mi9: Structure of the Phosphomimetic Mutant of the Elongation Factor Ef-Tu T62E

The structure of Structure of the Phosphomimetic Mutant of the Elongation Factor Ef-Tu T62E, PDB code: 5mi9 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)	51.04 / 3.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	58.120, 62.100, 65.470, 109.25, 106.00, 88.15
R / Rfree (%)	22.6 / 25.3

The binding sites of Magnesium atom in the Structure of the Phosphomimetic Mutant of the Elongation Factor Ef-Tu T62E (pdb code 5mi9). 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 the Phosphomimetic Mutant of the Elongation Factor Ef-Tu T62E, PDB code: 5mi9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Phosphomimetic Mutant of the Elongation Factor Ef-Tu T62E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Phosphomimetic Mutant of the Elongation Factor Ef-Tu T62E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:51.1 occ:1.00 O3B A:GDP402 1.9 70.6 1.0 O A:HOH502 1.9 5.1 1.0 O A:HOH501 2.3 14.3 1.0 OG1 A:THR26 2.3 65.6 1.0 O2B A:GDP402 2.8 66.5 1.0 PB A:GDP402 2.8 70.5 1.0 O A:HOH505 3.0 5.2 1.0 CB A:THR26 3.1 69.2 1.0 N A:THR26 3.6 62.4 1.0 O2A A:GDP402 3.7 72.1 1.0 O3A A:GDP402 3.8 69.1 1.0 CA A:THR26 3.9 63.1 1.0 OD1 A:ASP51 4.0 0.3 1.0 O1B A:GDP402 4.0 73.4 1.0 PA A:GDP402 4.1 74.1 1.0 O1A A:GDP402 4.1 74.7 1.0 OD2 A:ASP81 4.2 0.9 1.0 O A:HOH503 4.2 14.3 1.0 CG2 A:THR26 4.3 64.0 1.0 OD1 A:ASP81 4.6 0.4 1.0 C A:LYS25 4.6 68.8 1.0 CB A:LYS25 4.7 63.8 1.0 O A:CYS82 4.7 0.7 1.0 CG A:ASP81 4.8 0.9 1.0 O A:PRO83 4.9 0.9 1.0 NZ A:LYS25 4.9 50.5 1.0 CE A:LYS25 5.0 59.5 1.0 N A:LYS25 5.0 66.7 1.0 CA A:LYS25 5.0 64.4 1.0

Magnesium binding site 2 out of 2 in the Structure of the Phosphomimetic Mutant of the Elongation Factor Ef-Tu T62E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Phosphomimetic Mutant of the Elongation Factor Ef-Tu T62E within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:0.6 occ:1.00 OG1 B:THR26 2.1 59.1 1.0 O2A B:GDP402 2.2 0.6 1.0 O B:HOH503 2.3 11.0 1.0 O B:HOH504 2.4 0.5 1.0 O1B B:GDP402 2.7 0.9 1.0 CB B:THR26 2.8 73.4 1.0 PA B:GDP402 2.9 0.7 1.0 O1A B:GDP402 3.0 1.0 1.0 O3B B:GDP402 3.0 0.1 1.0 PB B:GDP402 3.1 0.0 1.0 O3A B:GDP402 3.3 0.7 1.0 O B:HOH502 3.7 36.0 1.0 N B:THR26 3.8 72.6 1.0 CA B:THR26 3.9 72.4 1.0 CG2 B:THR26 3.9 72.5 1.0 O B:HOH506 4.0 24.8 1.0 CE1 B:PHE47 4.2 0.8 1.0 CZ B:PHE47 4.2 0.5 1.0 O5' B:GDP402 4.4 0.3 1.0 O2B B:GDP402 4.6 0.1 1.0 C B:THR26 4.9 74.0 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