Magnesium in PDB 4ncf: Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (399-852) From Saccharomyces Cerevisiae in Complex with Gdp

The structure of Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (399-852) From Saccharomyces Cerevisiae in Complex with Gdp, PDB code: 4ncf 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)	46.66 / 3.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.560, 119.460, 120.730, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 28.1

The binding sites of Magnesium atom in the Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (399-852) From Saccharomyces Cerevisiae in Complex with Gdp (pdb code 4ncf). 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 (399-852) From Saccharomyces Cerevisiae in Complex with Gdp, PDB code: 4ncf:
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 (399-852) From Saccharomyces Cerevisiae 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 (399-852) From Saccharomyces Cerevisiae in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:86.7 occ:1.00 OG1 A:THR419 2.1 78.7 1.0 O3B A:GDP901 2.6 69.8 1.0 O1B A:GDP901 3.2 69.2 1.0 NZ A:LYS418 3.3 74.7 1.0 CB A:THR419 3.4 78.2 1.0 PB A:GDP901 3.4 68.8 1.0 O2B A:GDP901 4.2 68.2 1.0 CG2 A:THR419 4.2 80.3 1.0 CA A:THR419 4.4 73.0 1.0 N A:THR419 4.4 70.2 1.0 O2A A:GDP901 4.7 86.0 1.0 CE A:LYS418 4.7 70.7 1.0 O3A A:GDP901 4.8 0.6 1.0 CG A:LYS418 4.9 69.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Eukaryotic Translation Initiation Factor EIF5B (399-852) From Saccharomyces Cerevisiae 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 (399-852) From Saccharomyces Cerevisiae in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:92.0 occ:1.00 OG1 B:THR419 2.2 0.2 1.0 O1B B:GDP901 2.4 0.2 1.0 O2B B:GDP901 3.2 0.5 1.0 PB B:GDP901 3.3 0.2 1.0 CB B:THR419 3.5 0.1 1.0 CG2 B:THR477 3.9 0.2 1.0 O3B B:GDP901 4.0 0.3 1.0 CG2 B:THR419 4.3 0.1 1.0 CE B:LYS418 4.5 0.4 1.0 CA B:THR419 4.5 0.7 1.0 N B:THR419 4.5 98.8 1.0 O3A B:GDP901 4.7 0.3 1.0 O2A B:GDP901 4.8 97.6 1.0 OD1 B:ASP476 4.9 0.4 1.0 NZ B:LYS418 4.9 0.5 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