Magnesium 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:

Sodium

(Na)

1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Gamma Subunit of the Translation Initiation Factor 2 From Sulfolobus Solfataricus in Complex with Gdp and Formate Ion, PDB code: 6i5m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg519 b:24.9 occ:1.00 OG1 A:THR23 2.0 25.1 1.0 O1B A:GDP501 2.1 16.4 1.0 O A:HOH619 2.2 22.8 1.0 O A:HOH621 2.2 22.3 1.0 O A:HOH812 2.2 30.0 1.0 CB A:THR23 3.1 27.8 1.0 PB A:GDP501 3.4 22.1 1.0 O A:HOH823 3.7 29.9 1.0 O2B A:GDP501 3.7 14.2 1.0 O A:HOH897 3.9 39.7 1.0 N A:THR23 4.0 19.0 1.0 OD2 A:ASP93 4.0 30.2 1.0 OE1 A:GLU40 4.1 39.0 1.0 CA A:THR23 4.1 21.5 1.0 CG2 A:THR23 4.1 24.5 1.0 OD1 A:ASP93 4.2 28.1 1.0 O2A A:GDP501 4.2 21.0 1.0 O3B A:GDP501 4.4 21.1 1.0 O3A A:GDP501 4.5 18.8 1.0 CG A:ASP93 4.5 24.6 1.0 O2 A:FMT502 4.6 23.0 1.0 PA A:GDP501 4.7 18.7 1.0 O A:HOH616 4.7 28.9 1.0 O A:HOH702 4.8 24.3 1.0 O1A A:GDP501 4.9 21.0 1.0 CD A:GLU40 4.9 34.8 1.0 CE A:LYS22 4.9 15.6 1.0 OE2 A:GLU40 4.9 43.1 1.0 CB A:LYS22 5.0 17.6 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg520 b:5.0 occ:0.33 NE2 A:HIS187 1.8 21.3 1.0 O A:HOH896 2.0 21.3 0.3 CE1 A:HIS187 2.8 24.9 1.0 CD2 A:HIS187 2.9 17.9 1.0 ND1 A:HIS187 3.9 26.5 1.0 CG A:HIS187 4.0 21.5 1.0 CD2 A:LEU186 4.2 19.5 1.0 O A:HOH1015 4.6 37.6 0.3 CG A:LEU186 4.9 25.1 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