Magnesium in PDB 3a4m: Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase

The structure of Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase, PDB code: 3a4m was solved by Y.Araiso, R.Ishitani, D.Soll, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.50 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.156, 74.524, 64.817, 90.00, 113.37, 90.00
R / Rfree (%)	20.9 / 25.3

The structure of Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase (pdb code 3a4m). 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 Archaeal O-Phosphoseryl-Trna(Sec) Kinase, PDB code: 3a4m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase


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 Archaeal O-Phosphoseryl-Trna(Sec) Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:22.5 occ:1.00 O2B A:ADP301 2.1 15.2 1.0 O A:HOH269 2.1 16.4 1.0 O A:HOH268 2.2 17.3 1.0 O A:HOH280 2.2 19.2 1.0 OG A:SER18 2.2 19.9 1.0 O A:HOH279 2.3 18.7 1.0 PB A:ADP301 3.2 17.3 1.0 CB A:SER18 3.2 18.6 1.0 O3B A:ADP301 3.4 19.1 1.0 N A:SER18 3.8 18.5 1.0 CA A:SER18 4.1 18.8 1.0 O1A A:ADP301 4.1 21.3 1.0 O A:HOH307 4.1 29.5 1.0 OD2 A:ASP78 4.1 20.1 1.0 OD1 A:ASP78 4.2 20.2 1.0 O3A A:ADP301 4.3 18.4 1.0 O1B A:ADP301 4.4 16.4 1.0 PA A:ADP301 4.5 19.1 1.0 O A:HOH380 4.5 38.5 1.0 CG A:ASP78 4.5 18.3 1.0 O A:HOH356 4.6 31.6 1.0 CB A:LYS17 4.7 13.8 1.0 OD1 A:ASP41 4.7 34.2 1.0 O2A A:ADP301 4.8 17.9 1.0 NH1 A:ARG120 4.8 27.9 1.0 C A:LYS17 4.9 16.7 1.0 CE A:LYS17 4.9 17.8 1.0 NZ A:LYS17 5.0 17.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase


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 Archaeal O-Phosphoseryl-Trna(Sec) Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:23.9 occ:1.00 O B:HOH267 2.0 20.5 1.0 O1B B:ADP301 2.0 17.2 1.0 O B:HOH274 2.1 24.2 1.0 O B:HOH275 2.1 22.3 1.0 OG B:SER18 2.2 20.1 1.0 O B:HOH285 2.3 26.6 1.0 CB B:SER18 3.1 18.6 1.0 PB B:ADP301 3.2 23.2 1.0 O3B B:ADP301 3.5 19.1 1.0 N B:SER18 3.9 19.1 1.0 O1A B:ADP301 3.9 24.1 1.0 O B:HOH286 4.0 29.4 1.0 CA B:SER18 4.1 19.4 1.0 OD2 B:ASP78 4.1 22.2 1.0 OD1 B:ASP78 4.2 20.7 1.0 O2B B:ADP301 4.3 19.3 1.0 O3A B:ADP301 4.3 24.0 1.0 PA B:ADP301 4.5 24.1 1.0 CG B:ASP78 4.6 22.4 1.0 OD1 B:ASP41 4.7 34.5 1.0 O2A B:ADP301 4.9 23.3 1.0 CE B:LYS17 4.9 19.3 1.0 CB B:LYS17 4.9 17.4 1.0 NZ B:LYS17 4.9 20.4 1.0 C B:LYS17 4.9 17.4 1.0

Y.Araiso, R.L.Sherrer, R.Ishitani, J.M.L.Ho, D.Soll, O.Nureki. Structure of A Trna-Dependent Kinase Essential For Selenocysteine Decoding Proc.Natl.Acad.Sci.Usa V. 106 16215 2009.
ISSN: ISSN 0027-8424
PubMed: 19805283
DOI: 10.1073/PNAS.0908861106