Magnesium in PDB 3adc: Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 2)

The structure of Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 2), PDB code: 3adc 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)	28.21 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.824, 263.558, 46.122, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.7

The binding sites of Magnesium atom in the Crystal Structure of O-Phosphoseryl-Trna Kinase Complexed with Selenocysteine Trna and Amppnp (Crystal Type 2) (pdb code 3adc). 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 2), PDB code: 3adc:
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 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2003 b:93.0 occ:1.00 OG A:SER14 1.9 74.1 1.0 O3G A:ANP2001 2.0 0.4 1.0 O2B A:ANP2001 2.1 0.7 1.0 O A:HOH1001 2.1 94.6 1.0 O A:HOH1002 2.1 88.9 1.0 O A:HOH1003 2.1 70.4 1.0 CB A:SER14 3.1 69.0 1.0 PB A:ANP2001 3.2 0.8 1.0 PG A:ANP2001 3.2 0.2 1.0 N3B A:ANP2001 3.3 0.2 1.0 OD2 A:ASP74 3.5 86.3 1.0 OD1 A:ASP74 3.7 88.5 1.0 N A:SER14 3.7 72.8 1.0 CA A:SER14 3.9 73.5 1.0 CG A:ASP74 4.0 83.5 1.0 O2G A:ANP2001 4.1 0.7 1.0 O2A A:ANP2001 4.1 0.0 1.0 O1B A:ANP2001 4.2 99.7 1.0 O1G A:ANP2001 4.3 0.2 1.0 O3A A:ANP2001 4.4 0.1 1.0 OD2 A:ASP37 4.5 76.7 1.0 PA A:ANP2001 4.6 0.7 1.0 O1A A:ANP2001 4.7 0.1 1.0 CB A:LYS13 4.7 65.3 1.0 C A:LYS13 4.8 68.5 1.0 O A:HOH1009 4.8 60.0 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 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2004 b:77.7 occ:1.00 OG B:SER14 1.9 76.2 1.0 O3G B:ANP2002 2.0 0.7 1.0 O2B B:ANP2002 2.1 1.0 1.0 O B:HOH1006 2.1 78.0 1.0 O B:HOH1005 2.1 79.0 1.0 O B:HOH1004 2.1 70.2 1.0 CB B:SER14 3.1 75.2 1.0 PB B:ANP2002 3.2 0.6 1.0 PG B:ANP2002 3.2 0.4 1.0 N3B B:ANP2002 3.3 0.1 1.0 OD2 B:ASP74 3.6 78.7 1.0 N B:SER14 3.7 76.8 1.0 OD1 B:ASP74 3.7 79.9 1.0 CA B:SER14 3.9 76.0 1.0 O2G B:ANP2002 4.0 0.6 1.0 O2A B:ANP2002 4.1 95.3 1.0 CG B:ASP74 4.1 81.8 1.0 O1B B:ANP2002 4.2 0.9 1.0 O1G B:ANP2002 4.3 0.7 1.0 O3A B:ANP2002 4.4 94.7 1.0 OD2 B:ASP37 4.5 90.4 1.0 PA B:ANP2002 4.5 91.8 1.0 CB B:LYS13 4.6 75.7 1.0 O1A B:ANP2002 4.6 86.8 1.0 C B:LYS13 4.8 76.3 1.0 CE B:LYS13 5.0 69.0 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