Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1002 b:18.1 occ:1.00 O1G A:GTP1001 2.0 15.2 1.0 O2B A:GTP1001 2.1 13.0 1.0 O A:HOH1101 2.1 16.6 1.0 OG1 A:THR557 2.1 17.3 1.0 OG1 A:THR537 2.2 15.5 1.0 O A:HOH1102 2.2 16.3 1.0 CB A:THR537 3.1 14.8 1.0 CB A:THR557 3.2 17.3 1.0 PB A:GTP1001 3.2 16.5 1.0 PG A:GTP1001 3.2 17.7 1.0 O3B A:GTP1001 3.3 18.4 1.0 N A:THR537 3.8 13.8 1.0 N A:THR557 3.9 17.4 1.0 O3G A:GTP1001 4.0 16.0 1.0 CA A:THR537 4.0 15.7 1.0 O2A A:GTP1001 4.1 18.2 1.0 CA A:THR557 4.1 18.6 1.0 CG2 A:THR557 4.2 15.4 1.0 OE1 A:GLU552 4.2 22.1 1.0 OD2 A:ASP594 4.2 19.6 1.0 OE2 A:GLU552 4.2 22.8 1.0 CG2 A:THR537 4.2 14.9 1.0 O1B A:GTP1001 4.2 16.3 1.0 O3A A:GTP1001 4.3 17.6 1.0 O2G A:GTP1001 4.3 20.2 1.0 OD1 A:ASP594 4.4 18.5 1.0 NA A:NA1003 4.4 21.8 1.0 CE A:LYS536 4.5 12.4 1.0 PA A:GTP1001 4.5 15.5 1.0 O1A A:GTP1001 4.6 17.6 1.0 O A:THR595 4.6 15.3 1.0 CB A:LYS536 4.7 15.3 1.0 CD A:GLU552 4.7 18.2 1.0 CG A:ASP594 4.7 20.2 1.0 NH2 A:ARG806 4.8 25.4 1.0 C A:ILE556 4.9 17.6 1.0 C A:LYS536 4.9 13.3 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1002 b:18.4 occ:1.00 O1G B:GTP1001 1.9 18.1 1.0 O1B B:GTP1001 2.1 16.3 1.0 O B:HOH1101 2.1 15.5 1.0 OG1 B:THR537 2.1 18.6 1.0 O B:HOH1102 2.1 16.1 1.0 OG1 B:THR557 2.1 20.8 1.0 CB B:THR537 3.1 20.2 1.0 PG B:GTP1001 3.1 19.8 1.0 CB B:THR557 3.2 23.9 1.0 PB B:GTP1001 3.2 18.0 1.0 O3B B:GTP1001 3.4 20.0 1.0 N B:THR537 3.9 15.8 1.0 N B:THR557 3.9 20.0 1.0 O3G B:GTP1001 4.0 20.7 1.0 CA B:THR537 4.0 16.5 1.0 OD2 B:ASP594 4.1 20.4 1.0 O1A B:GTP1001 4.1 18.0 1.0 CA B:THR557 4.2 17.6 1.0 CG2 B:THR557 4.2 14.8 1.0 OE2 B:GLU552 4.2 21.4 1.0 CG2 B:THR537 4.2 21.3 1.0 O2B B:GTP1001 4.3 16.1 1.0 OE1 B:GLU552 4.3 22.6 1.0 O2G B:GTP1001 4.3 17.6 1.0 O3A B:GTP1001 4.4 15.8 1.0 OD1 B:ASP594 4.4 19.0 1.0 NA B:NA1003 4.4 20.3 1.0 CE B:LYS536 4.5 14.1 1.0 O B:THR595 4.5 18.5 1.0 PA B:GTP1001 4.6 18.6 1.0 CG B:ASP594 4.6 18.4 1.0 O2A B:GTP1001 4.7 19.8 1.0 CB B:LYS536 4.7 13.0 1.0 CD B:GLU552 4.7 20.7 1.0 NH2 B:ARG806 4.7 27.2 1.0 C B:LYS536 5.0 13.7 1.0 NZ B:LYS536 5.0 15.7 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