Sodium in PDB 4ncn: Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (517-858) From Chaetomium Thermophilum in Complex with Gtp

The structure of Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (517-858) From Chaetomium Thermophilum in Complex with Gtp, PDB code: 4ncn was solved by B.Kuhle, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.65 / 1.87
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.410, 114.840, 65.880, 90.00, 102.41, 90.00
R / Rfree (%)	16.4 / 20.4

The structure of Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (517-858) From Chaetomium Thermophilum in Complex with Gtp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (517-858) From Chaetomium Thermophilum in Complex with Gtp (pdb code 4ncn). 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 Eukaryotic Translation Initiation Factor EIF5B (517-858) From Chaetomium Thermophilum in Complex with Gtp, PDB code: 4ncn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (517-858) From Chaetomium Thermophilum in Complex with Gtp


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 Eukaryotic Translation Initiation Factor EIF5B (517-858) From Chaetomium Thermophilum in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1003 b:21.8 occ:1.00 O A:GLY555 2.3 22.2 1.0 OD2 A:ASP533 2.3 22.0 1.0 O3G A:GTP1001 2.4 16.0 1.0 O2A A:GTP1001 2.4 18.2 1.0 O3B A:GTP1001 2.5 18.4 1.0 PG A:GTP1001 3.1 17.7 1.0 O A:HOH1101 3.2 16.6 1.0 C A:GLY555 3.4 26.3 1.0 CA A:ILE556 3.5 19.4 1.0 PA A:GTP1001 3.5 15.5 1.0 CG A:ASP533 3.6 27.7 1.0 O3A A:GTP1001 3.6 17.6 1.0 PB A:GTP1001 3.6 16.5 1.0 CG2 A:ILE556 3.8 23.2 1.0 O1G A:GTP1001 3.9 15.2 1.0 O A:HOH1197 3.9 37.5 1.0 N A:ILE556 3.9 20.8 1.0 CA A:ASP533 3.9 22.7 1.0 C5' A:GTP1001 4.0 17.1 1.0 N A:ASP533 4.1 19.1 1.0 CB A:ILE556 4.1 24.2 1.0 O2B A:GTP1001 4.3 13.0 1.0 O5' A:GTP1001 4.3 16.9 1.0 NE2 A:GLN549 4.3 21.0 1.0 O2G A:GTP1001 4.4 20.2 1.0 CB A:ASP533 4.4 22.6 1.0 MG A:MG1002 4.4 18.1 1.0 OD1 A:ASP533 4.5 25.0 1.0 N A:THR557 4.5 17.4 1.0 C A:ILE556 4.5 17.6 1.0 CA A:GLY555 4.6 24.7 1.0 OE1 A:GLU552 4.7 22.1 1.0 CG2 A:VAL532 4.8 19.0 1.0 O1A A:GTP1001 4.8 17.6 1.0 O1B A:GTP1001 4.9 16.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (517-858) From Chaetomium Thermophilum in Complex with Gtp


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 Eukaryotic Translation Initiation Factor EIF5B (517-858) From Chaetomium Thermophilum in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1003 b:20.3 occ:1.00 OD2 B:ASP533 2.3 20.3 1.0 O B:GLY555 2.3 22.3 1.0 O1A B:GTP1001 2.4 18.0 1.0 O3G B:GTP1001 2.4 20.7 1.0 O3B B:GTP1001 2.5 20.0 1.0 PG B:GTP1001 3.1 19.8 1.0 O B:HOH1101 3.2 15.5 1.0 C B:GLY555 3.4 26.2 1.0 CG B:ASP533 3.5 27.9 1.0 CA B:ILE556 3.5 18.4 1.0 PA B:GTP1001 3.6 18.6 1.0 PB B:GTP1001 3.6 18.0 1.0 O3A B:GTP1001 3.6 15.8 1.0 C5' B:GTP1001 3.9 19.6 1.0 O1G B:GTP1001 4.0 18.1 1.0 O B:HOH1191 4.0 43.5 1.0 CA B:ASP533 4.0 19.2 1.0 N B:ILE556 4.0 19.5 1.0 CG2 B:ILE556 4.0 27.2 1.0 N B:ASP533 4.2 16.3 1.0 NE2 B:GLN549 4.2 21.0 1.0 O2G B:GTP1001 4.2 17.6 1.0 CB B:ILE556 4.2 27.2 1.0 O1B B:GTP1001 4.3 16.3 1.0 O5' B:GTP1001 4.3 20.1 1.0 CB B:ASP533 4.3 18.7 1.0 OD1 B:ASP533 4.4 26.7 1.0 MG B:MG1002 4.4 18.4 1.0 N B:THR557 4.5 20.0 1.0 C B:ILE556 4.5 24.3 1.0 CA B:GLY555 4.7 23.4 1.0 OE1 B:GLU552 4.7 22.6 1.0 O2B B:GTP1001 4.8 16.1 1.0 O2A B:GTP1001 4.8 19.8 1.0 CG2 B:VAL532 4.9 19.1 1.0

B.Kuhle, R.Ficner. EIF5B Employs A Novel Domain Release Mechanism to Catalyze Ribosomal Subunit Joining. Embo J. V. 33 1177 2014.
ISSN: ISSN 0261-4189
PubMed: 24686316
DOI: 10.1002/EMBJ.201387344