Magnesium in PDB 3add: Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 3)

The structure of Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 3), PDB code: 3add was solved by Y.Itoh, S.Chiba, S.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.55 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.860, 258.896, 45.704, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.8

The binding sites of Magnesium atom in the Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 3) (pdb code 3add). 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 O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 3), PDB code: 3add:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 3)


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 O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2003 b:59.6 occ:1.00 O A:HOH1001 2.0 53.8 1.0 O A:HOH1003 2.0 52.5 1.0 O A:HOH1002 2.1 39.5 1.0 O3G A:ANP2001 2.1 75.6 1.0 OG A:SER14 2.1 29.8 1.0 O2B A:ANP2001 2.2 46.5 1.0 CB A:SER14 3.2 34.5 1.0 PB A:ANP2001 3.3 48.6 1.0 PG A:ANP2001 3.3 85.1 1.0 N3B A:ANP2001 3.5 59.2 1.0 OD2 A:ASP74 3.8 59.1 1.0 OD1 A:ASP74 3.8 62.7 1.0 N A:SER14 3.8 34.1 1.0 O A:HOH1072 4.0 48.1 1.0 O2A A:ANP2001 4.0 62.9 1.0 CA A:SER14 4.0 32.4 1.0 O2G A:ANP2001 4.1 83.2 1.0 OD2 A:ASP37 4.2 47.7 1.0 CG A:ASP74 4.2 55.3 1.0 O1B A:ANP2001 4.2 53.3 1.0 O1G A:ANP2001 4.5 81.7 1.0 O3A A:ANP2001 4.5 52.2 1.0 PA A:ANP2001 4.7 60.5 1.0 CB A:LYS13 4.8 32.3 1.0 CE A:LYS13 4.8 35.8 1.0 C A:LYS13 4.9 37.0 1.0 O1A A:ANP2001 5.0 62.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 3)


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 O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2004 b:41.6 occ:1.00 O3G B:ANP2002 2.0 62.0 1.0 O2B B:ANP2002 2.1 37.7 1.0 O B:HOH1005 2.1 29.4 1.0 O B:HOH1004 2.1 24.1 1.0 OG B:SER14 2.1 41.5 1.0 O B:HOH1006 2.1 33.5 1.0 CB B:SER14 3.0 29.6 1.0 PB B:ANP2002 3.2 39.5 1.0 PG B:ANP2002 3.2 79.1 1.0 N3B B:ANP2002 3.3 43.9 1.0 N B:SER14 3.6 28.0 1.0 OD2 B:ASP74 3.7 57.0 1.0 O B:HOH1071 3.8 33.2 1.0 CA B:SER14 3.8 31.7 1.0 OD1 B:ASP74 4.1 50.1 1.0 O2G B:ANP2002 4.1 77.6 1.0 O2A B:ANP2002 4.1 44.0 1.0 O B:HOH1082 4.2 46.7 1.0 O1B B:ANP2002 4.3 41.5 1.0 CG B:ASP74 4.3 49.3 1.0 O1G B:ANP2002 4.3 74.1 1.0 OD2 B:ASP37 4.4 35.6 1.0 O3A B:ANP2002 4.4 44.1 1.0 PA B:ANP2002 4.6 46.1 1.0 CB B:LYS13 4.7 32.1 1.0 C B:LYS13 4.8 32.1 1.0 O1A B:ANP2002 4.8 43.4 1.0 CE B:LYS13 4.9 42.2 1.0

S.Chiba, Y.Itoh, S.Sekine, S.Yokoyama. Structural Basis For the Major Role of O-Phosphoseryl-Trna Kinase in the Uga-Specific Encoding of Selenocysteine Mol.Cell V. 39 410 2010.
ISSN: ISSN 1097-2765
PubMed: 20705242
DOI: 10.1016/J.MOLCEL.2010.07.018