Magnesium in PDB 4ncl: Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (517-970) From Chaetomium Thermophilum in Complex with Gdp

The structure of Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (517-970) From Chaetomium Thermophilum in Complex with Gdp, PDB code: 4ncl 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)	47.87 / 2.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.900, 72.960, 199.230, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (517-970) From Chaetomium Thermophilum in Complex with Gdp (pdb code 4ncl). 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 (517-970) From Chaetomium Thermophilum in Complex with Gdp, PDB code: 4ncl:
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 (517-970) From Chaetomium Thermophilum in Complex with Gdp


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 (517-970) From Chaetomium Thermophilum in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:75.5 occ:1.00 O A:HOH1192 2.4 66.8 1.0 OG1 A:THR537 2.7 73.6 1.0 O2B A:GDP1001 2.7 81.8 1.0 O A:HOH1191 3.4 62.7 1.0 CE A:LYS536 3.5 70.2 1.0 NZ A:LYS536 3.7 72.5 1.0 CG A:LYS536 3.9 68.3 1.0 PB A:GDP1001 3.9 85.4 1.0 CB A:THR537 4.0 71.8 1.0 O1B A:GDP1001 4.0 86.4 1.0 CB A:PRO596 4.1 90.6 1.0 CD A:LYS536 4.2 67.6 1.0 N A:THR537 4.5 67.8 1.0 O3B A:GDP1001 4.5 87.5 1.0 CA A:THR537 4.7 67.8 1.0 O2A A:GDP1001 4.7 0.1 1.0 CG A:PRO596 4.8 91.6 1.0 OD1 A:ASP594 4.9 80.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (517-970) From Chaetomium Thermophilum in Complex with Gdp


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 (517-970) From Chaetomium Thermophilum in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:71.0 occ:1.00 O B:HOH1167 2.1 63.5 1.0 O B:HOH1154 2.3 71.9 1.0 O3B B:GDP1001 2.9 80.7 1.0 O2B B:GDP1001 2.9 80.5 1.0 OG1 B:THR537 3.2 61.4 1.0 O B:HOH1200 3.5 64.2 1.0 PB B:GDP1001 3.5 80.0 1.0 O B:HOH1195 4.3 58.1 0.6 CB B:THR537 4.3 61.4 1.0 NZ B:LYS536 4.3 66.5 1.0 O1B B:GDP1001 4.4 79.7 1.0 CE B:LYS536 4.4 65.9 1.0 CB B:PRO596 4.5 87.0 1.0 O1A B:GDP1001 4.7 71.9 1.0 O3A B:GDP1001 4.7 0.7 1.0 N B:THR537 5.0 56.5 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