Magnesium in PDB 6ji2: Crystal Structure of Archaeal Ribosomal Protein AP1, Apelota, and Gtp- Bound AEF1A Complex

The structure of Crystal Structure of Archaeal Ribosomal Protein AP1, Apelota, and Gtp- Bound AEF1A Complex, PDB code: 6ji2 was solved by K.Maruyama, H.Imai, M.Kawamura, S.Ishino, Y.Ishino, K.Ito, T.Uchiumi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	106.42 / 3.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	71.447, 73.405, 108.142, 98.64, 93.80, 100.44
R / Rfree (%)	19.9 / 27.9

The structure of Crystal Structure of Archaeal Ribosomal Protein AP1, Apelota, and Gtp- Bound AEF1A Complex also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Archaeal Ribosomal Protein AP1, Apelota, and Gtp- Bound AEF1A Complex (pdb code 6ji2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Archaeal Ribosomal Protein AP1, Apelota, and Gtp- Bound AEF1A Complex, PDB code: 6ji2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Archaeal Ribosomal Protein AP1, Apelota, and Gtp- Bound AEF1A Complex


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 Archaeal Ribosomal Protein AP1, Apelota, and Gtp- Bound AEF1A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:64.8 occ:1.00 O2G A:GTP501 2.0 65.6 1.0 OG A:SER20 2.1 68.9 1.0 OG1 A:THR71 2.2 78.0 1.0 O2B A:GTP501 2.4 74.8 1.0 O A:HOH601 2.7 52.0 1.0 CB A:THR71 3.1 79.3 1.0 OD1 A:ASP90 3.2 66.2 1.0 CB A:SER20 3.3 73.9 1.0 OD2 A:ASP90 3.4 70.7 1.0 PG A:GTP501 3.4 69.8 1.0 PB A:GTP501 3.4 72.6 1.0 N A:SER20 3.5 76.1 1.0 O3B A:GTP501 3.7 71.1 1.0 CG A:ASP90 3.7 69.0 1.0 CB A:LYS19 3.7 80.3 1.0 O A:ALA91 3.8 63.4 1.0 CG2 A:THR71 3.9 80.3 1.0 CA A:SER20 3.9 75.8 1.0 NZ A:LYS19 3.9 83.5 1.0 O1B A:GTP501 4.2 69.5 1.0 O3G A:GTP501 4.3 71.5 1.0 C A:LYS19 4.3 77.9 1.0 CA A:THR71 4.4 78.3 1.0 OD1 A:ASP60 4.5 75.3 1.0 O1G A:GTP501 4.5 71.6 1.0 N A:THR71 4.5 79.3 1.0 CA A:LYS19 4.5 78.9 1.0 CD A:LYS19 4.6 83.8 1.0 NA A:NA503 4.7 60.3 1.0 CG A:LYS19 4.8 82.6 1.0 C A:ALA91 4.8 63.4 1.0 O3A A:GTP501 4.8 75.4 1.0 CE A:LYS19 4.8 83.2 1.0 N A:LYS19 4.9 77.9 1.0 O1A A:GTP501 5.0 77.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Archaeal Ribosomal Protein AP1, Apelota, and Gtp- Bound AEF1A Complex


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 Archaeal Ribosomal Protein AP1, Apelota, and Gtp- Bound AEF1A Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:52.6 occ:1.00 OG1 E:THR71 2.2 72.5 1.0 O2B E:GTP501 2.2 69.6 1.0 O2G E:GTP501 2.4 65.5 1.0 OG E:SER20 2.6 73.1 1.0 O E:HOH602 2.8 46.5 1.0 O3B E:GTP501 2.9 71.2 1.0 PB E:GTP501 3.1 71.0 1.0 NA E:NA503 3.1 71.9 1.0 PG E:GTP501 3.2 68.0 1.0 CB E:SER20 3.3 78.2 1.0 O1A E:GTP501 3.3 79.4 1.0 OD2 E:ASP60 3.4 84.8 1.0 CB E:THR71 3.5 73.3 1.0 N E:THR71 3.7 77.7 1.0 O3G E:GTP501 3.7 68.7 1.0 OD1 E:ASP60 3.9 84.5 1.0 O3A E:GTP501 3.9 74.9 1.0 PA E:GTP501 3.9 78.4 1.0 CG E:ASP60 4.1 83.9 1.0 CA E:THR71 4.1 75.3 1.0 O2A E:GTP501 4.3 75.4 1.0 N E:SER20 4.3 76.5 1.0 O1B E:GTP501 4.4 65.7 1.0 CA E:SER20 4.4 78.1 1.0 O1G E:GTP501 4.5 73.2 1.0 CG2 E:THR71 4.6 73.7 1.0 OD2 E:ASP90 4.6 63.3 1.0 C E:ILE70 4.7 79.5 1.0 CB E:ALA56 4.9 84.9 1.0

K.Maruyama, H.Imai, M.Kawamura, S.Ishino, Y.Ishino, K.Ito, T.Uchiumi. Switch of the Interactions Between the Ribosomal Stalk and EF1A in the Gtp- and Gdp-Bound Conformations. Sci Rep V. 9 14761 2019.
ISSN: ESSN 2045-2322
PubMed: 31611569
DOI: 10.1038/S41598-019-51266-X