Magnesium in PDB 3bjt: Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein

All present enzymatic activity of Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein:
2.7.1.40;

The structure of Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein, PDB code: 3bjt was solved by N.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.32 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	74.634, 80.707, 107.597, 69.82, 77.74, 67.97
R / Rfree (%)	21.1 / 27.1

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein (pdb code 3bjt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein, PDB code: 3bjt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:23.6 occ:1.00 OD2 A:ASP113 2.6 35.9 1.0 O A:THR114 2.8 28.4 1.0 O A:HOH902 2.8 23.0 1.0 OD1 A:ASN75 2.9 34.5 1.0 CG A:ASP113 3.5 34.8 1.0 OG A:SER77 3.6 42.4 1.0 C A:THR114 3.7 31.3 1.0 OG A:SER243 3.9 30.4 1.0 CG A:ASN75 3.9 32.5 1.0 CB A:SER77 3.9 37.4 1.0 O A:ASP113 4.0 30.4 1.0 CA A:LYS115 4.1 29.5 1.0 OD1 A:ASP113 4.1 35.0 1.0 O A:HOH909 4.2 26.4 1.0 NZ A:LYS270 4.2 30.5 1.0 ND2 A:ASN75 4.3 34.2 1.0 N A:LYS115 4.3 30.2 1.0 NH2 A:ARG73 4.3 38.9 1.0 O A:LYS115 4.3 31.5 1.0 N A:SER77 4.4 37.0 1.0 C A:ASP113 4.4 28.9 1.0 CB A:ASP113 4.5 29.8 1.0 C A:LYS115 4.6 31.0 1.0 OE1 A:GLU118 4.6 43.3 1.0 N A:THR114 4.7 29.8 1.0 CA A:SER77 4.8 37.9 1.0 CA A:THR114 4.8 32.1 1.0 N A:PHE76 4.8 35.8 1.0 CB A:SER243 4.9 29.9 1.0

Magnesium binding site 2 out of 4 in the Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:25.4 occ:1.00 O B:THR114 2.5 42.8 1.0 OG B:SER77 2.6 46.0 1.0 OD1 B:ASN75 2.7 39.0 1.0 OD2 B:ASP113 2.8 51.3 1.0 C B:THR114 3.4 43.9 1.0 CB B:SER77 3.7 44.7 1.0 CG B:ASP113 3.8 47.7 1.0 CG B:ASN75 3.8 36.5 1.0 OG B:SER243 3.9 39.7 1.0 CA B:LYS115 3.9 44.8 1.0 O B:ASP113 4.0 40.1 1.0 N B:LYS115 4.0 44.7 1.0 N B:SER77 4.1 46.6 1.0 C B:ASP113 4.2 42.3 1.0 O B:HOH926 4.3 47.3 1.0 CB B:ASP113 4.4 44.7 1.0 N B:PHE76 4.4 40.0 1.0 ND2 B:ASN75 4.4 36.1 1.0 N B:THR114 4.4 43.0 1.0 CA B:THR114 4.5 43.8 1.0 CA B:SER77 4.5 45.4 1.0 O B:LYS115 4.5 46.5 1.0 OD1 B:ASP113 4.6 47.1 1.0 C B:LYS115 4.6 45.4 1.0 NH1 B:ARG73 4.6 42.3 1.0 OE1 B:GLU118 4.6 57.4 1.0 NZ B:LYS270 4.6 29.4 1.0 C B:PHE76 4.8 45.0 1.0 CA B:ASN75 4.8 37.1 1.0 C B:ASN75 4.9 38.3 1.0 O B:HOH932 4.9 34.0 1.0 CB B:ASN75 4.9 36.8 1.0 CA B:ASP113 5.0 42.5 1.0

Magnesium binding site 3 out of 4 in the Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg904 b:31.8 occ:1.00 OD2 C:ASP113 1.8 51.0 1.0 OG C:SER77 2.6 50.7 1.0 OD1 C:ASN75 2.7 40.1 1.0 O C:THR114 3.0 43.9 1.0 CG C:ASP113 3.1 50.2 1.0 O C:HOH916 3.2 50.6 1.0 C C:THR114 3.7 43.8 1.0 OG C:SER243 3.7 45.1 1.0 OD1 C:ASP113 3.8 52.6 1.0 CG C:ASN75 3.8 39.1 1.0 CB C:SER77 3.9 48.6 1.0 CA C:LYS115 4.1 44.5 1.0 CB C:ASP113 4.2 46.5 1.0 N C:LYS115 4.2 44.4 1.0 NZ C:LYS270 4.2 37.1 1.0 O C:LYS115 4.3 45.5 1.0 ND2 C:ASN75 4.4 38.3 1.0 C C:ASP113 4.4 44.2 1.0 N C:SER77 4.4 47.4 1.0 O C:ASP113 4.4 44.0 1.0 N C:THR114 4.5 43.4 1.0 OE1 C:GLU118 4.6 58.2 1.0 C C:LYS115 4.6 44.2 1.0 CA C:SER77 4.6 48.9 1.0 CA C:THR114 4.7 42.4 1.0 N C:PHE76 4.7 42.5 1.0 NH2 C:ARG73 4.8 33.2 1.0 CB C:SER243 4.8 39.9 1.0 CA C:ASP113 4.9 44.8 1.0 C C:PHE76 5.0 46.0 1.0

Magnesium binding site 4 out of 4 in the Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg905 b:31.5 occ:1.00 OD2 D:ASP113 2.1 48.4 1.0 OD1 D:ASN75 2.7 40.9 1.0 O D:THR114 2.9 50.6 1.0 CG D:ASP113 3.3 48.3 1.0 CB D:SER77 3.6 42.5 1.0 CG D:ASN75 3.7 37.0 1.0 C D:THR114 3.8 50.5 1.0 CA D:LYS115 4.0 48.6 1.0 OD1 D:ASP113 4.0 49.5 1.0 OG D:SER243 4.0 46.9 1.0 NZ D:LYS270 4.1 34.0 1.0 O D:ASP113 4.2 49.7 1.0 N D:LYS115 4.3 50.8 1.0 N D:SER77 4.3 40.8 1.0 ND2 D:ASN75 4.3 35.4 1.0 CB D:ASP113 4.3 46.7 1.0 O D:LYS115 4.5 48.4 1.0 C D:ASP113 4.5 47.8 1.0 CA D:SER77 4.5 41.5 1.0 OG D:SER77 4.6 48.9 1.0 C D:LYS115 4.6 49.4 1.0 NH2 D:ARG73 4.6 43.1 1.0 OE1 D:GLU118 4.6 51.4 1.0 N D:PHE76 4.8 42.1 1.0 N D:THR114 4.8 49.7 1.0 CB D:ASN75 4.9 36.8 1.0 CA D:ASN75 4.9 38.5 1.0 CA D:THR114 4.9 49.5 1.0 O4 D:OXL904 5.0 52.9 1.0

H.R.Christofk, M.G.Vander Heiden, N.Wu, J.M.Asara, L.C.Cantley. Pyruvate Kinase M2 Is A Phosphotyrosine-Binding Protein. Nature V. 452 181 2008.
ISSN: ISSN 0028-0836
PubMed: 18337815
DOI: 10.1038/NATURE06667