Magnesium in PDB 8fr3: E. Coli Ef-Tu in Complex with Kkl-55

The structure of E. Coli Ef-Tu in Complex with Kkl-55, PDB code: 8fr3 was solved by H.A.Nguyen, A.B.Kuzmishin Nagy, C.M.Dunham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.82 / 2.23
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.385, 65.222, 70.559, 107.67, 98.79, 107.08
R / Rfree (%)	24.5 / 27.5

The structure of E. Coli Ef-Tu in Complex with Kkl-55 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the E. Coli Ef-Tu in Complex with Kkl-55 (pdb code 8fr3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the E. Coli Ef-Tu in Complex with Kkl-55, PDB code: 8fr3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E. Coli Ef-Tu in Complex with Kkl-55


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Ef-Tu in Complex with Kkl-55 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:63.9 occ:1.00 O2B A:GDP502 2.1 54.1 1.0 OG1 A:THR25 2.1 59.4 1.0 PB A:GDP502 3.2 45.5 1.0 CB A:THR25 3.4 55.7 1.0 O1B A:GDP502 3.5 51.8 1.0 O A:CYS81 3.7 67.1 1.0 N A:THR25 4.1 46.1 1.0 CA A:PRO82 4.1 67.1 1.0 O3B A:GDP502 4.2 52.4 1.0 O A:PRO82 4.3 71.1 1.0 CA A:THR25 4.3 54.2 1.0 O1A A:GDP502 4.3 51.5 1.0 OD2 A:ASP80 4.3 66.8 1.0 CG2 A:THR25 4.4 58.2 1.0 O3A A:GDP502 4.4 55.7 1.0 C A:CYS81 4.5 63.2 1.0 OD1 A:ASP80 4.6 66.5 1.0 N A:PRO82 4.7 64.2 1.0 C A:PRO82 4.7 63.4 1.0 PA A:GDP502 4.7 52.6 1.0 OD1 A:ASP50 4.7 70.7 1.0 NZ A:LYS24 4.7 45.2 1.0 CE A:LYS24 4.8 46.4 1.0 CB A:LYS24 4.9 50.7 1.0 CG A:ASP80 4.9 67.0 1.0 O2A A:GDP502 5.0 50.1 1.0

Magnesium binding site 2 out of 2 in the E. Coli Ef-Tu in Complex with Kkl-55


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Ef-Tu in Complex with Kkl-55 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:62.1 occ:1.00 OG1 B:THR25 2.0 58.1 1.0 O2B B:GDP502 2.0 54.3 1.0 CB B:THR25 3.2 54.0 1.0 PB B:GDP502 3.3 54.0 1.0 O1B B:GDP502 3.5 48.0 1.0 O B:CYS81 3.9 61.6 1.0 CA B:PRO82 4.1 68.8 1.0 N B:THR25 4.1 54.5 1.0 CG2 B:THR25 4.1 60.7 1.0 O1A B:GDP502 4.1 45.3 1.0 CA B:THR25 4.2 51.0 1.0 OD2 B:ASP80 4.3 60.8 1.0 O3B B:GDP502 4.3 58.2 1.0 O B:PRO82 4.4 63.9 1.0 OD1 B:ASP50 4.4 73.5 1.0 O3A B:GDP502 4.4 47.2 1.0 C B:CYS81 4.6 60.1 1.0 PA B:GDP502 4.7 57.0 1.0 OD1 B:ASP80 4.7 55.5 1.0 N B:PRO82 4.7 65.2 1.0 C B:PRO82 4.8 62.7 1.0 CG B:ASP80 4.9 61.0 1.0 O2A B:GDP502 4.9 58.8 1.0 CB B:PRO82 5.0 61.7 1.0

N.Marathe, H.A.Nguyen, J.N.Alumasa, A.B.Kuzmishin Nagy, M.Vazquez, C.M.Dunham, K.C.Keiler. Antibiotic That Inhibits Trans -Translation Blocks Binding of Ef-Tu to Tmrna But Not to Trna. Mbio 46123 2023.
ISSN: ESSN 2150-7511
PubMed: 37681945
DOI: 10.1128/MBIO.01461-23