Magnesium in PDB 7l21: Pyruvate Kinase M2 Mutant-N70D

All present enzymatic activity of Pyruvate Kinase M2 Mutant-N70D:
2.7.1.40;

The structure of Pyruvate Kinase M2 Mutant-N70D, PDB code: 7l21 was solved by S.Nandi, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.81 / 2.29
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	139.336, 158.303, 241.611, 90, 90, 90
R / Rfree (%)	18.3 / 22.9

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Mutant-N70D (pdb code 7l21). 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 Mutant-N70D, PDB code: 7l21:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pyruvate Kinase M2 Mutant-N70D


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 Mutant-N70D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:23.8 occ:1.00 O4 A:OXL601 2.0 32.2 1.0 O A:HOH756 2.1 20.2 1.0 OD2 A:ASP296 2.1 21.0 1.0 O3 A:OXL601 2.1 22.5 1.0 OE1 A:GLU272 2.2 19.9 1.0 O A:HOH747 2.2 27.7 1.0 C2 A:OXL601 2.7 31.2 1.0 C1 A:OXL601 2.7 24.1 1.0 CG A:ASP296 3.2 24.6 1.0 CD A:GLU272 3.2 21.1 1.0 OE2 A:GLU272 3.7 23.1 1.0 CB A:ASP296 3.7 19.5 1.0 O2 A:OXL601 3.8 33.2 1.0 O1 A:OXL601 4.0 24.1 1.0 NZ A:LYS270 4.0 24.0 1.0 O3 A:GOL603 4.2 41.6 1.0 O A:HOH860 4.3 25.3 1.0 CZ A:PHE244 4.3 28.2 1.0 OD1 A:ASP296 4.3 23.7 1.0 N A:ASP296 4.5 17.1 1.0 CG A:GLU272 4.6 18.2 1.0 CE A:LYS270 4.6 17.7 1.0 CB A:ALA293 4.6 15.8 1.0 CE2 A:PHE244 4.6 29.4 1.0 CA A:ASP296 4.7 21.2 1.0 CE1 A:PHE244 4.8 22.1 1.0 CB A:GLU272 4.9 21.1 1.0

Magnesium binding site 2 out of 4 in the Pyruvate Kinase M2 Mutant-N70D


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 Mutant-N70D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:24.2 occ:1.00 OD2 B:ASP296 1.9 23.0 1.0 O4 B:OXL601 2.0 26.4 1.0 O B:HOH772 2.2 26.5 1.0 O B:HOH755 2.2 21.8 1.0 OE1 B:GLU272 2.2 20.1 1.0 O3 B:OXL601 2.4 21.7 1.0 C2 B:OXL601 2.8 31.9 1.0 C1 B:OXL601 3.0 22.9 1.0 CG B:ASP296 3.1 27.2 1.0 CD B:GLU272 3.2 21.0 1.0 OE2 B:GLU272 3.6 19.2 1.0 CB B:ASP296 3.7 21.8 1.0 O2 B:OXL601 4.0 30.5 1.0 OD1 B:ASP296 4.1 27.2 1.0 CZ B:PHE244 4.2 26.8 1.0 O1 B:OXL601 4.2 22.1 1.0 NZ B:LYS270 4.3 20.6 1.0 CE2 B:PHE244 4.4 26.8 1.0 N B:ASP296 4.4 18.8 1.0 O3 B:GOL603 4.5 31.1 1.0 O B:HOH857 4.5 39.8 1.0 CG B:GLU272 4.6 19.6 1.0 O B:HOH721 4.6 21.2 1.0 CA B:ASP296 4.7 17.8 1.0 CE B:LYS270 4.7 20.0 1.0 CB B:GLU272 4.8 23.0 1.0 CB B:ALA293 4.9 15.2 1.0 CE1 B:PHE244 4.9 21.8 1.0

Magnesium binding site 3 out of 4 in the Pyruvate Kinase M2 Mutant-N70D


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 Mutant-N70D within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:19.4 occ:1.00 O C:HOH718 1.9 19.7 1.0 O4 C:OXL601 2.0 23.2 1.0 OE1 C:GLU272 2.2 23.7 1.0 O C:HOH783 2.2 20.8 1.0 OD2 C:ASP296 2.2 18.5 1.0 O3 C:OXL601 2.3 23.1 1.0 C2 C:OXL601 2.7 29.6 1.0 C1 C:OXL601 2.9 21.4 1.0 CD C:GLU272 3.2 19.9 1.0 CG C:ASP296 3.3 23.7 1.0 OE2 C:GLU272 3.5 19.8 1.0 CB C:ASP296 3.7 21.3 1.0 O2 C:OXL601 3.9 36.5 1.0 NZ C:LYS270 4.1 21.9 1.0 O1 C:OXL601 4.1 22.0 1.0 CE1 C:PHE244 4.2 32.2 1.0 OD1 C:ASP296 4.4 22.5 1.0 N C:ASP296 4.4 20.2 1.0 O C:HOH768 4.4 22.3 1.0 CG C:GLU272 4.5 19.4 1.0 O C:HOH850 4.5 31.2 1.0 CE C:LYS270 4.6 18.9 1.0 CB C:ALA293 4.6 19.3 1.0 CB C:GLU272 4.7 21.5 1.0 CA C:ASP296 4.7 21.4 1.0 CZ C:PHE244 4.7 26.4 1.0 CD1 C:PHE244 4.9 29.7 1.0

Magnesium binding site 4 out of 4 in the Pyruvate Kinase M2 Mutant-N70D


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 Mutant-N70D within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:36.0 occ:1.00 OD2 D:ASP296 2.0 28.5 1.0 OE1 D:GLU272 2.3 32.2 1.0 O4 D:OXL601 2.4 30.8 1.0 O3 D:OXL601 2.4 35.2 1.0 C1 D:OXL601 3.0 35.9 1.0 C2 D:OXL601 3.0 31.8 1.0 CG D:ASP296 3.2 34.3 1.0 CD D:GLU272 3.3 33.3 1.0 OE2 D:GLU272 3.5 28.3 1.0 CB D:ASP296 3.9 28.9 1.0 NZ D:LYS270 4.0 30.2 1.0 O1 D:OXL601 4.1 42.2 1.0 CZ D:PHE244 4.1 36.3 1.0 OD1 D:ASP296 4.2 32.3 1.0 O2 D:OXL601 4.3 25.6 1.0 CE2 D:PHE244 4.3 35.5 1.0 O D:HOH754 4.3 34.9 1.0 CE D:LYS270 4.5 26.2 1.0 CG D:GLU272 4.6 28.4 1.0 CE1 D:PHE244 4.8 35.0 1.0 N D:ASP296 4.8 18.0 1.0 CB D:GLU272 4.9 29.6 1.0 CB D:ALA293 4.9 24.4 1.0 CA D:ASP296 5.0 26.0 1.0

S.Nandi, M.Dey. Mechanistic Insights Into the Signal Communication Between the Active Site and Amino Acid Binding Site of PKM2 To Be Published.