Magnesium in PDB 5w75: Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168

The structure of Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168, PDB code: 5w75 was solved by E.A.Ortlund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.71 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.417, 173.420, 208.178, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22

The binding sites of Magnesium atom in the Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168 (pdb code 5w75). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168, PDB code: 5w75:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:31.8 occ:1.00 O A:HOH521 2.1 30.1 1.0 O3B A:GDP401 2.1 33.7 1.0 O A:HOH504 2.2 28.6 1.0 O A:HOH554 2.3 32.5 1.0 OG A:SER26 2.3 33.2 1.0 O A:HOH556 2.3 34.5 1.0 PB A:GDP401 3.0 31.8 1.0 O1B A:GDP401 3.1 39.3 1.0 CB A:SER26 3.1 28.7 1.0 O3A A:GDP401 3.7 43.1 1.0 N A:SER26 3.7 30.9 1.0 CA A:SER26 4.0 29.4 1.0 OD1 A:ASP81 4.0 33.0 1.0 O A:CYS82 4.0 34.3 1.0 O A:HOH503 4.1 42.3 1.0 O A:HOH541 4.3 25.6 1.0 OD1 A:ASP51 4.4 41.1 1.0 O A:HOH591 4.4 33.5 1.0 O2B A:GDP401 4.5 38.3 1.0 OD2 A:ASP81 4.5 36.5 1.0 O2A A:GDP401 4.5 25.9 1.0 PA A:GDP401 4.5 31.9 1.0 CA A:PRO83 4.5 33.7 1.0 O1A A:GDP401 4.6 35.9 1.0 CE A:LYS25 4.6 29.0 1.0 CG A:ASP81 4.7 32.5 1.0 CB A:LYS25 4.7 23.1 1.0 C A:LYS25 4.8 33.4 1.0 O A:PRO83 4.8 38.1 1.0 C A:CYS82 4.8 33.4 1.0 NZ A:LYS25 4.9 29.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:37.5 occ:1.00 O B:HOH513 2.1 33.1 1.0 O B:HOH520 2.1 31.4 1.0 O B:HOH511 2.1 36.1 1.0 OG B:SER26 2.1 33.3 1.0 O B:HOH539 2.2 32.7 1.0 O1B B:GDP401 2.2 40.9 1.0 CB B:SER26 3.1 35.6 1.0 PB B:GDP401 3.1 36.8 1.0 O3B B:GDP401 3.2 38.6 1.0 N B:SER26 3.7 35.9 1.0 O3A B:GDP401 3.7 49.5 1.0 CA B:SER26 4.0 35.0 1.0 O B:CYS82 4.0 38.9 1.0 OD2 B:ASP81 4.0 34.9 1.0 OD1 B:ASP51 4.2 46.7 1.0 O B:HOH540 4.3 32.0 1.0 OD1 B:ASP81 4.4 37.9 1.0 O1A B:GDP401 4.5 37.2 1.0 PA B:GDP401 4.5 40.5 1.0 CA B:PRO83 4.5 34.8 1.0 O2A B:GDP401 4.5 40.4 1.0 O2B B:GDP401 4.6 47.7 1.0 O B:HOH537 4.6 45.5 1.0 CG B:ASP81 4.6 41.1 1.0 CB B:LYS25 4.7 31.8 1.0 O B:PRO83 4.7 36.5 1.0 C B:LYS25 4.7 37.5 1.0 NZ B:LYS25 4.8 37.5 1.0 C B:CYS82 4.8 34.6 1.0 CE B:LYS25 4.9 32.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:37.1 occ:1.00 O C:HOH505 2.1 33.4 1.0 OG C:SER26 2.1 31.4 1.0 O C:HOH548 2.1 33.1 1.0 O3B C:GDP401 2.1 43.5 1.0 O C:HOH517 2.1 40.4 1.0 O C:HOH502 2.2 37.6 1.0 PB C:GDP401 3.1 39.6 1.0 CB C:SER26 3.1 28.3 1.0 O1B C:GDP401 3.2 37.1 1.0 O3A C:GDP401 3.7 51.3 1.0 N C:SER26 3.7 36.2 1.0 OD2 C:ASP81 3.9 35.6 1.0 O C:CYS82 4.0 38.6 1.0 CA C:SER26 4.0 30.5 1.0 OD1 C:ASP51 4.1 53.4 1.0 O C:HOH551 4.2 31.9 1.0 CA C:PRO83 4.4 38.9 1.0 OD1 C:ASP81 4.5 38.7 1.0 O C:HOH538 4.5 46.3 1.0 O2A C:GDP401 4.5 38.0 1.0 O2B C:GDP401 4.5 43.5 1.0 PA C:GDP401 4.5 41.3 1.0 CG C:ASP81 4.6 38.7 1.0 O1A C:GDP401 4.6 47.2 1.0 C C:CYS82 4.7 37.8 1.0 CB C:LYS25 4.7 33.7 1.0 O C:PRO83 4.8 45.6 1.0 C C:LYS25 4.8 37.8 1.0 CE C:LYS25 4.9 26.5 1.0 N C:PRO83 4.9 37.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Reconstructed Bacterial Elongation Factor Node 168 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:38.2 occ:1.00 O D:HOH567 2.0 35.2 1.0 O D:HOH513 2.1 28.9 1.0 O2B D:GDP401 2.2 37.8 1.0 OG D:SER26 2.2 33.8 1.0 O D:HOH522 2.2 32.5 1.0 PB D:GDP401 3.4 38.8 1.0 CB D:SER26 3.5 31.3 1.0 O3B D:GDP401 3.6 42.8 1.0 O D:CYS82 3.7 33.8 1.0 CA D:PRO83 4.0 37.0 1.0 OD1 D:ASP51 4.1 43.0 1.0 O D:PRO83 4.2 38.0 1.0 O D:HOH557 4.2 30.9 1.0 O2A D:GDP401 4.2 34.8 1.0 OD1 D:ASP81 4.2 38.4 1.0 N D:SER26 4.2 33.8 1.0 O1B D:GDP401 4.3 38.9 1.0 C D:CYS82 4.4 33.3 1.0 CA D:SER26 4.4 26.8 1.0 OD2 D:ASP81 4.5 36.1 1.0 O3A D:GDP401 4.5 41.9 1.0 C D:PRO83 4.6 37.8 1.0 N D:PRO83 4.6 35.3 1.0 CG D:ASP81 4.8 37.1 1.0 PA D:GDP401 4.8 35.3 1.0 O D:HOH606 4.9 34.4 1.0 CE D:LYS25 4.9 32.5 1.0 O1A D:GDP401 4.9 38.0 1.0

C.D.Okafor, M.C.Pathak, C.E.Fagan, N.C.Bauer, M.F.Cole, E.A.Gaucher, E.A.Ortlund. Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus. Structure V. 26 118 2018.
ISSN: ISSN 1878-4186
PubMed: 29276038
DOI: 10.1016/J.STR.2017.11.018