Sodium in PDB 6i5m: Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion

The structure of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion, PDB code: 6i5m was solved by O.Kravchenko, O.Nikonov, A.Gabdulkhakov, E.Stolboushkina, V.Arkhipova, M.Garber, S.Nikonov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.24 / 2.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	142.143, 142.143, 218.587, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 22.4

The structure of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion (pdb code 6i5m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion, PDB code: 6i5m:

Sodium binding site 1 out of 1 in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Na521 b:31.2 occ:1.00 O A:VAL154 2.2 23.5 1.0 O A:VAL151 2.3 23.4 1.0 O A:HOH919 2.4 31.1 1.0 C A:VAL154 3.4 27.1 1.0 C A:VAL151 3.4 22.9 1.0 N A:VAL154 4.0 19.9 1.0 CG2 A:VAL154 4.2 23.4 1.0 N A:ASP152 4.2 22.1 1.0 CA A:VAL154 4.2 26.1 1.0 CA A:VAL151 4.3 26.7 1.0 CA A:ASP152 4.3 25.8 1.0 N A:SER155 4.3 28.4 1.0 C A:SER155 4.3 28.3 1.0 C A:ASP152 4.4 29.9 1.0 CA A:SER155 4.4 27.6 1.0 CB A:VAL151 4.4 27.4 1.0 O A:SER155 4.4 26.0 1.0 O A:ASP152 4.7 32.5 1.0 N A:VAL153 4.8 28.3 1.0 N A:LYS156 4.8 23.9 1.0 O A:HOH952 4.8 42.4 1.0 CB A:VAL154 4.9 27.7 1.0

O.Nikonov, O.Kravchenko, N.Nevskaya, E.Stolboushkina, M.Garber, S.Nikonov. The Third Structural Switch in the Archaeal Translation Initiation Factor 2 (AIF2) Molecule and Its Possible Role in the Initiation of Gtp Hydrolysis and the Removal of AIF2 From the Ribosome. Acta Crystallogr D Struct V. 75 392 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 30988256
DOI: 10.1107/S2059798319002304