Magnesium in PDB 5mi8: Structure of the Phosphomimetic Mutant of Ef-Tu T383E

The structure of Structure of the Phosphomimetic Mutant of Ef-Tu T383E, PDB code: 5mi8 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)	52.75 / 2.18
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.870, 61.510, 65.040, 71.53, 71.17, 87.76
R / Rfree (%)	18.7 / 22.5

The structure of Structure of the Phosphomimetic Mutant of Ef-Tu T383E also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Structure of the Phosphomimetic Mutant of Ef-Tu T383E (pdb code 5mi8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Phosphomimetic Mutant of Ef-Tu T383E, PDB code: 5mi8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Phosphomimetic Mutant of Ef-Tu T383E


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 Ef-Tu T383E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:43.7 occ:1.00 O A:HOH507 2.0 33.6 1.0 O A:HOH535 2.0 46.0 1.0 O3B A:GDP403 2.0 37.7 1.0 O A:HOH513 2.0 41.0 1.0 OG1 A:THR26 2.1 51.1 1.0 O A:HOH528 2.2 39.2 1.0 PB A:GDP403 3.2 38.2 1.0 CB A:THR26 3.3 47.4 1.0 O2B A:GDP403 3.4 43.7 1.0 N A:THR26 3.8 37.4 1.0 OD2 A:ASP81 4.0 58.8 1.0 O A:CYS82 4.1 42.6 1.0 CA A:THR26 4.1 38.4 1.0 O1B A:GDP403 4.2 38.4 1.0 O3A A:GDP403 4.2 40.8 1.0 O A:PRO83 4.2 54.2 1.0 OD1 A:ASP51 4.3 73.6 1.0 O2A A:GDP403 4.3 36.5 1.0 CA A:PRO83 4.3 49.2 1.0 CG2 A:THR26 4.4 49.6 1.0 OD1 A:ASP81 4.4 48.4 1.0 PA A:GDP403 4.6 45.3 1.0 CG A:ASP81 4.6 50.7 1.0 O A:HOH525 4.7 38.9 1.0 O1A A:GDP403 4.7 45.3 1.0 CB A:LYS25 4.7 35.9 1.0 O A:HOH533 4.7 50.6 1.0 C A:PRO83 4.8 52.8 1.0 C A:CYS82 4.8 47.5 1.0 C A:LYS25 4.8 38.2 1.0 NZ A:LYS25 4.9 39.2 1.0 CE A:LYS25 4.9 42.4 1.0 N A:PRO83 5.0 48.6 1.0

Magnesium binding site 2 out of 4 in the Structure of the Phosphomimetic Mutant of Ef-Tu T383E


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 Ef-Tu T383E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:58.1 occ:1.00 O A:HOH530 2.2 48.5 1.0 O A:HOH520 2.3 44.5 1.0 O A:HOH503 2.4 43.3 1.0 OD1 A:ASP355 2.4 52.1 1.0 CG A:ASP355 3.7 55.4 1.0 OD2 A:ASP355 4.3 63.3 1.0 O A:GLY354 4.4 50.0 1.0 C A:GLY354 4.5 48.7 1.0 O A:PRO353 4.6 48.0 1.0 N A:ASP355 4.7 42.5 1.0 CB A:ASP355 4.8 44.3 1.0 CA A:ASP355 4.8 41.6 1.0 O A:HOH578 5.0 50.0 1.0

Magnesium binding site 3 out of 4 in the Structure of the Phosphomimetic Mutant of Ef-Tu T383E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Phosphomimetic Mutant of Ef-Tu T383E within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:46.6 occ:1.00 O B:HOH502 2.0 48.4 1.0 OG1 B:THR26 2.0 51.9 1.0 O B:HOH506 2.0 50.1 1.0 O B:HOH503 2.0 47.8 1.0 O1B B:GDP403 2.0 51.1 1.0 O B:HOH539 2.1 63.8 1.0 CB B:THR26 3.2 53.7 1.0 PB B:GDP403 3.3 52.9 1.0 O3B B:GDP403 3.6 56.7 1.0 OD2 B:ASP81 3.8 69.2 1.0 N B:THR26 3.9 47.4 1.0 O2A B:GDP403 4.0 54.5 1.0 CA B:THR26 4.1 47.9 1.0 OD1 B:ASP51 4.1 87.2 1.0 O B:CYS82 4.1 53.9 1.0 O B:HOH515 4.1 59.9 1.0 CG2 B:THR26 4.2 52.2 1.0 O B:PRO83 4.3 59.6 1.0 O3A B:GDP403 4.3 52.1 1.0 CA B:PRO83 4.3 55.2 1.0 O2B B:GDP403 4.4 60.0 1.0 OD1 B:ASP81 4.4 66.0 1.0 CG B:ASP81 4.5 62.9 1.0 PA B:GDP403 4.6 52.1 1.0 O1A B:GDP403 4.7 52.4 1.0 CB B:LYS25 4.8 40.8 1.0 C B:PRO83 4.8 59.9 1.0 C B:CYS82 4.8 55.5 1.0 C B:LYS25 4.9 47.9 1.0 N B:PRO83 4.9 54.5 1.0

Magnesium binding site 4 out of 4 in the Structure of the Phosphomimetic Mutant of Ef-Tu T383E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Phosphomimetic Mutant of Ef-Tu T383E within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:63.7 occ:1.00 O B:HOH521 2.1 49.1 1.0 O B:HOH519 2.3 45.4 1.0 OD2 B:ASP142 4.2 70.0 1.0 OD1 B:ASP142 4.3 62.2 1.0 CG B:ASP142 4.7 63.5 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