Sodium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Archaeal Ribosomal Protein AP1, Apelota, and Gtp- Bound AEF1A Complex, PDB code: 6ji2:
Jump to Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na503 b:60.3 occ:1.00 O3B A:GTP501 2.1 71.1 1.0 O1A A:GTP501 2.2 77.6 1.0 O A:HOH601 2.6 52.0 1.0 OD1 A:ASP16 2.6 73.8 1.0 O A:GLY69 2.9 70.1 1.0 O3G A:GTP501 3.0 71.5 1.0 O3A A:GTP501 3.1 75.4 1.0 PG A:GTP501 3.1 69.8 1.0 PB A:GTP501 3.1 72.6 1.0 PA A:GTP501 3.2 78.4 1.0 O2B A:GTP501 3.6 74.8 1.0 C A:GLY69 3.7 74.0 1.0 O2G A:GTP501 3.9 65.6 1.0 C5' A:GTP501 3.9 76.0 1.0 CG A:ASP16 3.9 72.9 1.0 CA A:ILE70 4.0 80.0 1.0 O5' A:GTP501 4.1 78.5 1.0 O1G A:GTP501 4.2 71.6 1.0 N A:ILE70 4.2 78.4 1.0 N A:THR71 4.3 79.3 1.0 CE1 A:PHE53 4.3 87.3 1.0 O1B A:GTP501 4.4 69.5 1.0 CA A:ASP16 4.4 73.0 1.0 OD2 A:ASP60 4.5 79.1 1.0 O2A A:GTP501 4.5 72.5 1.0 C A:ILE70 4.6 80.5 1.0 N A:ASP16 4.7 73.7 1.0 MG A:MG502 4.7 64.8 1.0 CD1 A:ILE70 4.7 87.6 1.0 OD2 A:ASP16 4.8 67.7 1.0 CD1 A:PHE53 4.8 88.5 1.0 CB A:ASP16 4.8 73.7 1.0 OG1 A:THR71 4.9 78.0 1.0 CA A:GLY69 4.9 73.9 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na503 b:71.9 occ:1.00 O3B E:GTP501 2.1 71.2 1.0 O1A E:GTP501 2.3 79.4 1.0 O E:GLY69 2.6 77.6 1.0 OD1 E:ASP16 2.7 73.9 1.0 O3G E:GTP501 3.0 68.7 1.0 MG E:MG502 3.1 52.6 1.0 PG E:GTP501 3.1 68.0 1.0 PB E:GTP501 3.3 71.0 1.0 O3A E:GTP501 3.3 74.9 1.0 PA E:GTP501 3.4 78.4 1.0 C E:GLY69 3.6 80.7 1.0 O2B E:GTP501 3.8 69.6 1.0 O2G E:GTP501 3.8 65.5 1.0 CG E:ASP16 3.9 77.7 1.0 CA E:ILE70 3.9 80.9 1.0 C5' E:GTP501 4.0 83.1 1.0 N E:ILE70 4.1 80.4 1.0 CE1 E:PHE53 4.1 96.6 1.0 O5' E:GTP501 4.2 83.3 1.0 O1G E:GTP501 4.2 73.2 1.0 N E:THR71 4.3 77.7 1.0 CD1 E:ILE70 4.4 85.0 1.0 CA E:ASP16 4.4 79.3 1.0 O1B E:GTP501 4.5 65.7 1.0 C E:ILE70 4.5 79.5 1.0 N E:ASP16 4.6 79.4 1.0 O2A E:GTP501 4.6 75.4 1.0 OD2 E:ASP60 4.6 84.8 1.0 CD1 E:PHE53 4.7 97.0 1.0 OD2 E:ASP16 4.7 75.5 1.0 CB E:ASP16 4.7 79.2 1.0 OG1 E:THR71 4.8 72.5 1.0 CA E:GLY69 4.9 81.5 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