Magnesium in PDB 3bjf: 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: 3bjf was solved by N.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.29 / 2.03
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	80.756, 81.458, 106.885, 74.63, 69.91, 66.10
R / Rfree (%)	20.8 / 24.6

The structure of Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Is A Phosphotyrosine Binding Protein (pdb code 3bjf). 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: 3bjf:
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:Mg701 b:15.5 occ:1.00 OD2 A:ASP113 2.7 27.3 1.0 OD1 A:ASN75 2.7 28.4 1.0 O A:THR114 2.7 24.3 1.0 O A:HOH902 2.8 21.8 1.0 OG A:SER77 3.5 37.6 1.0 OG A:SER243 3.6 21.7 1.0 CG A:ASP113 3.7 25.9 1.0 C A:THR114 3.7 25.7 1.0 CG A:ASN75 3.8 28.4 1.0 NZ A:LYS270 3.8 21.5 1.0 O A:ASP113 3.9 23.6 1.0 CB A:SER77 4.0 36.1 1.0 CA A:LYS115 4.2 26.7 1.0 O A:HOH964 4.3 28.3 1.0 C A:ASP113 4.3 23.6 1.0 N A:LYS115 4.3 25.8 1.0 N A:SER77 4.4 33.2 1.0 ND2 A:ASN75 4.4 30.0 1.0 OD1 A:ASP113 4.4 23.3 1.0 CB A:ASP113 4.5 25.0 1.0 O A:LYS115 4.6 26.9 1.0 NH1 A:ARG73 4.6 29.5 1.0 OE1 A:GLU118 4.6 37.7 1.0 N A:THR114 4.7 24.4 1.0 N A:PHE76 4.7 28.5 1.0 CA A:THR114 4.7 24.0 1.0 C A:LYS115 4.8 25.9 1.0 CB A:SER243 4.8 20.4 1.0 CA A:SER77 4.8 34.4 1.0 CA A:ASN75 4.9 27.3 1.0 CB A:ASN75 5.0 27.1 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:Mg702 b:8.6 occ:1.00 OD2 B:ASP113 2.6 19.8 1.0 OD1 B:ASN75 2.7 17.2 1.0 O B:HOH904 2.7 13.9 1.0 OG B:SER77 2.7 24.5 1.0 O B:THR114 2.8 18.1 1.0 O B:HOH1009 2.8 27.9 1.0 C B:THR114 3.6 17.1 1.0 OG B:SER243 3.7 14.2 1.0 CG B:ASN75 3.7 19.6 1.0 CG B:ASP113 3.7 19.9 1.0 CB B:SER77 3.8 22.3 1.0 O B:ASP113 3.8 17.1 1.0 NZ B:LYS270 3.9 13.0 1.0 CA B:LYS115 4.1 19.7 1.0 OE1 B:GLU118 4.1 26.0 1.0 N B:SER77 4.2 21.1 1.0 N B:LYS115 4.2 18.0 1.0 C B:ASP113 4.2 17.1 1.0 O B:HOH1069 4.3 32.0 1.0 ND2 B:ASN75 4.3 19.9 1.0 O B:LYS115 4.5 17.4 1.0 K B:K602 4.5 45.4 1.0 CA B:SER77 4.5 22.0 1.0 OD1 B:ASP113 4.5 16.7 1.0 CB B:ASP113 4.5 17.4 1.0 N B:THR114 4.6 17.2 1.0 NH1 B:ARG73 4.6 27.4 1.0 CA B:THR114 4.7 16.6 1.0 C B:LYS115 4.7 18.6 1.0 N B:PHE76 4.8 18.7 1.0 CB B:SER243 4.9 15.1 1.0 CB B:ASN75 4.9 16.7 1.0 CA B:ASN75 4.9 16.9 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:Mg703 b:12.7 occ:1.00 OD2 C:ASP113 2.6 25.9 1.0 O C:THR114 2.7 22.7 1.0 O C:HOH904 2.7 19.6 1.0 OD1 C:ASN75 2.8 23.5 1.0 C C:THR114 3.6 22.6 1.0 OG C:SER243 3.6 20.0 1.0 CG C:ASP113 3.7 23.1 1.0 CB C:SER77 3.7 28.8 1.0 CG C:ASN75 3.8 22.2 1.0 O C:ASP113 3.8 19.3 1.0 NZ C:LYS270 3.9 22.1 1.0 CA C:LYS115 4.1 23.2 1.0 N C:LYS115 4.2 21.5 1.0 OG C:SER77 4.2 35.4 1.0 N C:SER77 4.2 25.5 1.0 C C:ASP113 4.2 20.8 1.0 ND2 C:ASN75 4.4 24.5 1.0 O C:LYS115 4.4 24.5 1.0 CB C:ASP113 4.5 21.7 1.0 OD1 C:ASP113 4.5 20.9 1.0 K C:K603 4.5 61.4 1.0 CA C:SER77 4.6 27.4 1.0 N C:THR114 4.6 21.6 1.0 OE1 C:GLU118 4.6 27.3 1.0 NH1 C:ARG73 4.6 29.6 1.0 CA C:THR114 4.6 21.0 1.0 C C:LYS115 4.6 25.0 1.0 N C:PHE76 4.8 21.2 1.0 CB C:SER243 4.8 17.1 1.0 CB C:ASN75 4.9 20.3 1.0 CA C:ASP113 5.0 21.8 1.0 CA C:ASN75 5.0 20.9 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:Mg704 b:15.4 occ:1.00 O D:HOH997 2.6 20.3 1.0 OD2 D:ASP113 2.7 20.9 1.0 O D:HOH905 2.7 17.6 1.0 OD1 D:ASN75 2.8 21.0 1.0 O D:THR114 2.8 19.2 1.0 OG D:SER243 3.6 20.3 1.0 C D:THR114 3.7 21.9 1.0 CG D:ASP113 3.7 21.2 1.0 CG D:ASN75 3.8 20.6 1.0 CB D:SER77 3.8 26.5 1.0 O D:ASP113 3.8 20.3 1.0 O D:HOH1016 3.8 30.3 1.0 OG D:SER77 4.0 34.8 1.0 NZ D:LYS270 4.0 18.5 1.0 CA D:LYS115 4.1 23.9 1.0 K D:K604 4.2 49.6 1.0 N D:LYS115 4.2 22.6 1.0 ND2 D:ASN75 4.2 22.4 1.0 C D:ASP113 4.2 20.8 1.0 N D:SER77 4.3 25.2 1.0 OE1 D:GLU118 4.4 32.5 1.0 OD1 D:ASP113 4.4 17.0 1.0 O D:LYS115 4.4 21.6 1.0 CB D:ASP113 4.5 19.1 1.0 CA D:SER77 4.6 26.7 1.0 N D:THR114 4.6 20.6 1.0 C D:LYS115 4.7 23.1 1.0 CA D:THR114 4.7 21.4 1.0 CB D:SER243 4.7 19.6 1.0 NH1 D:ARG73 4.8 22.9 1.0 N D:PHE76 4.9 19.9 1.0 CB D:ASN75 4.9 17.8 1.0 CA D:ASN75 5.0 18.4 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