Magnesium in PDB 4ac9: Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp

The structure of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp, PDB code: 4ac9 was solved by M.Leibundgut, C.Frick, M.Thanbichler, A.Boeck, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.975 / 3.03
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	146.920, 146.920, 297.480, 90.00, 90.00, 120.00
R / Rfree (%)	18.99 / 22.21

The structure of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp also contains other interesting chemical elements:

Mercury

(Hg)

16 atoms

The binding sites of Magnesium atom in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp (pdb code 4ac9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp, PDB code: 4ac9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis 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 Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1470 b:0.3 occ:0.89 O2B A:GDP1469 2.0 100.0 0.9 O A:HOH2003 2.0 0.5 0.9 O A:HOH2002 2.0 0.1 0.9 O A:HOH2004 2.1 0.6 0.9 O A:HOH2001 2.1 0.9 0.9 OG1 A:THR19 2.1 0.9 1.0 PB A:GDP1469 3.2 0.3 0.9 O3B A:GDP1469 3.2 86.3 0.9 CB A:THR19 3.3 0.5 1.0 N A:THR19 3.8 0.0 1.0 CA A:THR19 4.0 0.3 1.0 O1B A:GDP1469 4.1 80.4 0.9 O2A A:GDP1469 4.2 94.4 0.9 O A:PRO67 4.3 0.7 1.0 O3A A:GDP1469 4.3 79.7 0.9 CG2 A:THR19 4.4 86.5 1.0 CE A:LYS18 4.5 0.6 1.0 CB A:LYS18 4.5 75.4 1.0 PA A:GDP1469 4.7 93.6 0.9 NZ A:LYS18 4.8 0.4 1.0 C A:LYS18 4.9 0.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis 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 Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1470 b:0.1 occ:0.90 O B:HOH2001 2.0 0.2 0.9 O B:HOH2003 2.0 98.2 0.9 O B:HOH2002 2.1 77.8 0.9 O B:HOH2004 2.1 71.6 0.9 O2B B:GDP1469 2.1 82.5 0.9 OG1 B:THR19 2.1 0.8 1.0 PB B:GDP1469 3.1 86.2 0.9 O3B B:GDP1469 3.2 0.0 0.9 CB B:THR19 3.4 96.2 1.0 O2A B:GDP1469 3.8 97.7 0.9 CG2 B:THR19 3.9 93.5 1.0 O3A B:GDP1469 3.9 79.5 0.9 N B:THR19 4.0 0.9 1.0 CA B:THR19 4.3 92.2 1.0 O1B B:GDP1469 4.3 97.1 0.9 PA B:GDP1469 4.4 77.6 0.9 CB B:LYS18 4.7 88.4 1.0 CE B:LYS18 4.7 77.8 1.0 O1A B:GDP1469 4.8 88.2 0.9 O B:PRO67 5.0 0.2 1.0 NZ B:LYS18 5.0 0.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Translation Elongation Factor Selb From Methanococcus Maripaludis in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1470 b:0.3 occ:0.68 OG1 C:THR19 2.0 92.0 1.0 O C:HOH2001 2.0 92.7 0.7 O C:HOH2004 2.0 0.9 0.7 O C:HOH2003 2.0 0.7 0.7 O C:HOH2002 2.0 0.4 0.7 O2B C:GDP1469 2.1 73.0 0.7 PB C:GDP1469 3.2 86.5 0.7 CB C:THR19 3.2 84.5 1.0 O3B C:GDP1469 3.3 89.5 0.7 N C:THR19 3.7 78.2 1.0 CA C:THR19 3.9 85.7 1.0 O1B C:GDP1469 4.0 74.6 0.7 O2A C:GDP1469 4.2 0.1 0.7 CG2 C:THR19 4.3 74.7 1.0 O3A C:GDP1469 4.4 62.0 0.7 CB C:LYS18 4.4 75.1 1.0 CE C:LYS18 4.5 0.6 1.0 NZ C:LYS18 4.6 0.4 1.0 PA C:GDP1469 4.7 99.7 0.7 C C:LYS18 4.7 87.4 1.0 O1A C:GDP1469 4.8 77.7 0.7

M.Leibundgut, C.Frick, M.Thanbichler, A.Bock, N.Ban. Selenocysteine Trna-Specific Elongation Factor Selb Is A Structural Chimaera of Elongation and Initiation Factors. Embo J. V. 24 11 2005.
ISSN: ISSN 0261-4189
PubMed: 15616587
DOI: 10.1038/SJ.EMBOJ.7600505