Sodium in PDB 6h6k: The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution.

The structure of The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution., PDB code: 6h6k was solved by O.Nikonov, O.Kravchenko, N.Nevskaya, E.Stolboushkina, A.Gabdulkhakov, M.Garber, S.Nikonov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.03 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	76.710, 76.750, 146.790, 101.46, 92.08, 95.97
R / Rfree (%)	21.6 / 24.8

The binding sites of Sodium atom in the The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution. (pdb code 6h6k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution., PDB code: 6h6k:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:51.0 occ:1.00 O A:HOH842 2.4 56.5 1.0 O A:MET111 2.4 35.9 1.0 O A:HOH777 2.5 45.9 1.0 O A:HOH808 2.5 72.6 1.0 O A:HOH678 2.6 43.7 1.0 O A:HOH675 2.8 51.7 1.0 C A:MET111 3.6 42.4 1.0 N A:ASP112 4.4 34.2 1.0 CA A:ASP112 4.4 38.3 1.0 N A:MET111 4.5 38.4 1.0 OD1 A:ASP112 4.5 35.8 1.0 O A:HOH841 4.5 61.7 1.0 O A:ALA109 4.5 39.1 1.0 CA A:MET111 4.6 33.9 1.0 O A:HOH762 4.6 51.1 1.0 O A:HOH830 4.7 56.0 1.0 CG2 A:VAL141 4.7 45.5 1.0 O A:HOH772 4.7 49.2 1.0 O A:ALA108 4.9 35.6 1.0 C A:LEU110 5.0 42.5 1.0 O A:HOH703 5.0 44.6 1.0

Sodium binding site 2 out of 6 in the The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:44.2 occ:1.00 OG1 A:THR54 2.4 36.6 1.0 O A:HOH662 2.4 40.5 1.0 O A:HOH815 2.4 49.5 1.0 O A:HOH776 2.6 40.8 1.0 O A:THR70 2.6 37.4 1.0 O A:HOH670 2.7 44.0 1.0 CB A:THR54 3.4 29.5 1.0 C A:THR70 3.7 36.8 1.0 CB A:THR70 3.7 41.0 1.0 CA A:THR54 4.0 33.7 1.0 OG1 A:THR70 4.1 39.6 1.0 O A:THR30 4.1 35.4 1.0 N A:ASN55 4.2 34.8 1.0 CA A:THR70 4.2 33.9 1.0 O A:HOH722 4.4 58.8 1.0 O A:ASN55 4.4 35.0 1.0 O A:ILE29 4.6 38.5 1.0 C A:THR54 4.7 35.2 1.0 CG2 A:THR54 4.7 24.7 1.0 CA A:THR30 4.7 31.6 1.0 C A:THR30 4.7 35.7 1.0 O A:HOH695 4.8 47.6 1.0 N A:GLU71 4.8 39.2 1.0 O A:HOH786 4.8 42.0 1.0 CG2 A:THR70 4.8 37.8 1.0 O A:GLU53 5.0 32.6 1.0 O A:HOH813 5.0 47.0 1.0

Sodium binding site 3 out of 6 in the The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:43.1 occ:1.00 O A:VAL151 2.3 35.5 1.0 O A:VAL154 2.4 33.7 1.0 C A:VAL151 3.5 33.6 1.0 C A:VAL154 3.6 37.4 1.0 C A:SER155 3.9 39.4 1.0 N A:LYS156 4.1 41.0 1.0 O A:SER155 4.1 42.9 1.0 CA A:SER155 4.2 40.5 1.0 CB A:VAL151 4.3 31.6 1.0 N A:SER155 4.3 39.0 1.0 N A:ASP152 4.3 35.6 1.0 CA A:VAL151 4.4 37.1 1.0 CA A:ASP152 4.4 40.5 1.0 N A:VAL154 4.5 35.9 1.0 CA A:VAL154 4.6 37.6 1.0 CG2 A:VAL154 4.6 42.3 1.0 CA A:LYS156 4.6 41.7 1.0 C A:ASP152 4.7 39.5 1.0 CG2 A:VAL151 4.7 33.9 1.0 O A:ASP152 5.0 35.3 1.0

Sodium binding site 4 out of 6 in the The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:40.1 occ:1.00 O B:VAL151 2.3 35.2 1.0 O B:VAL154 2.4 34.4 1.0 C B:VAL151 3.5 37.3 1.0 C B:VAL154 3.6 39.3 1.0 C B:SER155 4.0 38.2 1.0 N B:LYS156 4.2 44.9 1.0 O B:SER155 4.2 43.7 1.0 CA B:SER155 4.3 41.6 1.0 N B:ASP152 4.3 36.5 1.0 CA B:ASP152 4.3 39.7 1.0 N B:SER155 4.4 42.8 1.0 CB B:VAL151 4.4 36.2 1.0 CA B:VAL151 4.4 42.1 1.0 N B:VAL154 4.4 36.8 1.0 CA B:VAL154 4.6 42.2 1.0 C B:ASP152 4.6 40.0 1.0 CA B:LYS156 4.7 39.9 1.0 CG2 B:VAL154 4.7 42.3 1.0 CG2 B:VAL151 4.8 37.2 1.0 O B:ASP152 4.9 35.2 1.0

Sodium binding site 5 out of 6 in the The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:46.2 occ:1.00 OG1 B:THR54 2.4 36.7 1.0 O B:HOH776 2.4 48.0 1.0 O B:HOH649 2.5 37.3 1.0 O B:HOH727 2.5 38.2 1.0 O B:HOH693 2.5 43.7 1.0 O B:THR70 2.6 38.6 1.0 CB B:THR54 3.4 29.3 1.0 CB B:THR70 3.7 43.1 1.0 C B:THR70 3.7 36.5 1.0 CA B:THR54 4.0 32.7 1.0 OG1 B:THR70 4.1 41.6 1.0 O B:THR30 4.2 35.8 1.0 N B:ASN55 4.2 35.5 1.0 CA B:THR70 4.2 37.1 1.0 O B:ASN55 4.3 31.9 1.0 C B:THR54 4.6 28.9 1.0 O B:ILE29 4.7 37.7 1.0 O B:HOH680 4.7 46.7 1.0 CG2 B:THR54 4.7 28.8 1.0 O B:HOH739 4.7 43.9 1.0 O B:HOH677 4.7 60.5 1.0 CA B:THR30 4.7 36.2 1.0 C B:THR30 4.8 38.7 1.0 CG2 B:THR70 4.8 36.6 1.0 N B:GLU71 4.8 38.9 1.0 O B:GLU53 4.9 35.4 1.0 O B:HOH788 4.9 49.4 1.0

Sodium binding site 6 out of 6 in the The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of the Fkr Mutant of the Archaeal Translation Initiation Factor 2 Gamma Subunit in Complex with Gdpcp, Obtained in the Absence of Magnesium Salts in the Crystallization Solution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:51.0 occ:1.00 OD2 B:ASP192 2.3 44.9 1.0 O B:HOH625 2.4 47.2 1.0 O B:TYR68 2.4 40.5 1.0 O B:GLU66 2.5 41.8 1.0 O B:HOH769 2.7 49.2 1.0 C B:GLU66 3.5 43.2 1.0 CG B:ASP192 3.5 56.8 1.0 C B:TYR68 3.6 41.3 1.0 CG1 B:VAL69 4.0 42.0 1.0 CA B:GLU66 4.0 38.1 1.0 N B:TYR68 4.2 39.8 1.0 CB B:ASP192 4.3 41.7 1.0 OD1 B:ASP192 4.4 47.1 1.0 N B:VAL69 4.4 36.5 1.0 CA B:VAL69 4.4 30.2 1.0 C B:ALA67 4.5 44.3 1.0 CA B:TYR68 4.5 32.9 1.0 O B:PRO65 4.5 37.2 1.0 N B:ALA67 4.5 42.4 1.0 OG B:SER76 4.7 49.1 1.0 O B:HOH741 4.8 40.1 1.0 CB B:GLU66 4.8 43.4 1.0 CB B:VAL69 4.8 37.3 1.0 CA B:ALA67 4.9 47.9 1.0 O B:ALA67 4.9 38.4 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