Magnesium in PDB 3a4l: Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase

The structure of Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase, PDB code: 3a4l 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)	46.37 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.134, 74.452, 64.698, 90.00, 113.64, 90.00
R / Rfree (%)	21 / 24.9

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 3a4l). 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: 3a4l:
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:21.4 occ:1.00 O3G A:ANP301 2.0 19.9 1.0 O1B A:ANP301 2.1 14.9 1.0 OG A:SER18 2.1 18.6 1.0 O A:HOH272 2.2 15.7 1.0 O A:HOH278 2.3 18.2 1.0 O A:HOH298 2.3 18.7 1.0 CB A:SER18 3.2 15.7 1.0 PG A:ANP301 3.2 20.2 1.0 PB A:ANP301 3.2 17.6 1.0 N3B A:ANP301 3.4 22.6 1.0 N A:SER18 3.8 18.4 1.0 O A:HOH267 3.9 31.2 1.0 O A:HOH321 4.0 26.6 1.0 CA A:SER18 4.1 17.6 1.0 O1A A:ANP301 4.1 22.4 1.0 OD1 A:ASP78 4.1 19.1 1.0 OD2 A:ASP78 4.1 21.7 1.0 O2G A:ANP301 4.1 20.5 1.0 O A:HOH345 4.2 37.7 1.0 O A:HOH361 4.3 29.8 1.0 O3A A:ANP301 4.3 19.5 1.0 O2B A:ANP301 4.3 17.0 1.0 O1G A:ANP301 4.4 25.1 1.0 CG A:ASP78 4.5 20.3 1.0 PA A:ANP301 4.5 20.5 1.0 OD1 A:ASP41 4.7 34.6 1.0 CB A:LYS17 4.7 16.0 1.0 O2A A:ANP301 4.8 18.9 1.0 C A:LYS17 4.9 17.4 1.0 CE A:LYS17 5.0 17.3 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:23.4 occ:1.00 O B:HOH267 2.1 18.4 1.0 O2G B:ANP301 2.1 23.1 1.0 O1B B:ANP301 2.1 18.9 1.0 OG B:SER18 2.2 17.5 1.0 O B:HOH393 2.2 24.0 1.0 O B:HOH283 2.3 22.8 1.0 CB B:SER18 3.2 20.2 1.0 PG B:ANP301 3.3 24.0 1.0 PB B:ANP301 3.3 22.2 1.0 N3B B:ANP301 3.5 23.2 1.0 N B:SER18 3.9 18.6 1.0 OD1 B:ASP78 4.0 20.4 1.0 O B:HOH358 4.0 31.1 1.0 O1G B:ANP301 4.0 24.6 1.0 O1A B:ANP301 4.1 24.3 1.0 CA B:SER18 4.1 20.4 1.0 O B:HOH285 4.2 35.8 1.0 OD2 B:ASP78 4.2 21.9 1.0 O2B B:ANP301 4.3 20.4 1.0 O3A B:ANP301 4.4 23.8 1.0 O3G B:ANP301 4.4 26.6 1.0 CG B:ASP78 4.5 21.1 1.0 PA B:ANP301 4.6 24.3 1.0 OD2 B:ASP41 4.6 31.6 1.0 O B:HOH338 4.7 27.0 1.0 CE B:LYS17 4.8 18.2 1.0 CB B:LYS17 4.8 19.9 1.0 O2A B:ANP301 4.9 21.4 1.0 C B:LYS17 5.0 17.1 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