Magnesium in PDB 6wp4: Pyruvate Kinase M2 Mutant-S37E

All present enzymatic activity of Pyruvate Kinase M2 Mutant-S37E:
2.7.1.40;

The structure of Pyruvate Kinase M2 Mutant-S37E, PDB code: 6wp4 was solved by S.Nandi, M.Razzaghi, D.Srivastava, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.53 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.167, 132.628, 110.128, 90.00, 112.74, 90.00
R / Rfree (%)	18.9 / 22.1

The structure of Pyruvate Kinase M2 Mutant-S37E also contains other interesting chemical elements:

Potassium	(K)	5 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Mutant-S37E (pdb code 6wp4). 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-S37E, PDB code: 6wp4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pyruvate Kinase M2 Mutant-S37E


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-S37E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:24.8 occ:1.00 O A:HOH787 2.0 22.4 1.0 O A:HOH779 2.0 25.6 1.0 O1 A:OXL606 2.1 31.0 1.0 OE1 A:GLU272 2.1 20.4 1.0 O2 A:OXL606 2.1 25.2 1.0 OD2 A:ASP296 2.2 27.8 1.0 C1 A:OXL606 2.8 29.9 1.0 C2 A:OXL606 2.8 26.1 1.0 CD A:GLU272 3.2 24.1 1.0 CG A:ASP296 3.3 27.1 1.0 OE2 A:GLU272 3.5 22.8 1.0 CB A:ASP296 3.8 17.8 1.0 NZ A:LYS270 4.0 21.8 1.0 O4 A:OXL606 4.1 26.8 1.0 O3 A:OXL606 4.1 32.4 1.0 N A:ASP296 4.3 17.7 1.0 CZ A:PHE244 4.3 26.7 1.0 O A:HOH861 4.4 41.6 1.0 OD1 A:ASP296 4.4 25.3 1.0 CE A:LYS270 4.5 20.9 1.0 O1 A:GOL612 4.5 40.1 1.0 O A:HOH783 4.5 20.6 1.0 CG A:GLU272 4.5 18.7 1.0 CA A:ASP296 4.7 19.9 1.0 CB A:ALA293 4.7 20.7 1.0 CB A:GLU272 4.7 22.0 1.0 CE2 A:PHE244 4.7 27.0 1.0 CE1 A:PHE244 4.8 27.3 1.0

Magnesium binding site 2 out of 4 in the Pyruvate Kinase M2 Mutant-S37E


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-S37E within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:27.7 occ:1.00 OD2 B:ASP296 2.1 24.4 1.0 OE1 B:GLU272 2.1 21.9 1.0 O B:HOH729 2.1 20.5 1.0 O B:HOH724 2.1 23.8 1.0 CD B:GLU272 3.1 26.6 1.0 CG B:ASP296 3.1 24.8 1.0 OE2 B:GLU272 3.5 24.5 1.0 CB B:ASP296 3.6 20.2 1.0 O B:HOH822 4.1 31.1 1.0 NZ B:LYS270 4.1 21.6 1.0 OD1 B:ASP296 4.2 25.9 1.0 N B:ASP296 4.3 23.0 1.0 CZ B:PHE244 4.3 27.1 1.0 CG B:GLU272 4.4 22.3 1.0 CE B:LYS270 4.5 22.0 1.0 CA B:ASP296 4.6 21.7 1.0 CB B:GLU272 4.6 23.9 1.0 O B:HOH764 4.6 23.2 1.0 CB B:ALA293 4.7 22.0 1.0 CE1 B:PHE244 4.8 30.8 1.0 CE2 B:PHE244 4.8 31.9 1.0

Magnesium binding site 3 out of 4 in the Pyruvate Kinase M2 Mutant-S37E


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-S37E within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:35.6 occ:1.00 O C:HOH828 2.1 26.1 1.0 OE1 C:GLU272 2.1 25.3 1.0 CD C:GLU272 3.1 28.0 1.0 CG C:ASP296 3.3 28.4 1.0 OE2 C:GLU272 3.5 25.2 1.0 CB C:ASP296 3.7 24.8 1.0 O C:HOH819 3.9 30.4 1.0 NZ C:LYS270 3.9 22.2 1.0 CZ C:PHE244 4.3 27.0 1.0 N C:ASP296 4.3 25.6 1.0 CE C:LYS270 4.4 22.4 1.0 O1 C:GOL608 4.4 40.1 1.0 CG C:GLU272 4.5 24.2 1.0 O C:HOH743 4.6 24.8 1.0 CE2 C:PHE244 4.6 30.4 1.0 CB C:ALA293 4.7 23.7 1.0 CA C:ASP296 4.7 24.5 1.0 CB C:GLU272 4.7 27.5 1.0 C1 C:GOL608 4.8 40.4 1.0 CE1 C:PHE244 4.9 28.7 1.0

Magnesium binding site 4 out of 4 in the Pyruvate Kinase M2 Mutant-S37E


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-S37E within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg604 b:31.0 occ:1.00 O D:HOH757 2.0 27.2 1.0 O D:HOH722 2.0 28.3 1.0 OD2 D:ASP296 2.0 32.0 1.0 O4 D:OXL607 2.2 33.8 1.0 OE1 D:GLU272 2.2 28.6 1.0 O3 D:OXL607 2.2 25.4 1.0 C1 D:OXL607 2.9 26.6 1.0 C2 D:OXL607 2.9 33.4 1.0 CG D:ASP296 3.1 30.6 1.0 CD D:GLU272 3.2 28.4 1.0 OE2 D:GLU272 3.5 24.9 1.0 CB D:ASP296 3.6 21.7 1.0 CZ D:PHE244 4.1 29.3 1.0 O1 D:OXL607 4.1 25.6 1.0 NZ D:LYS270 4.1 24.6 1.0 O2 D:OXL607 4.1 36.5 1.0 OD1 D:ASP296 4.2 29.1 1.0 CE2 D:PHE244 4.4 32.4 1.0 N D:ASP296 4.4 24.4 1.0 O D:HOH719 4.5 26.3 1.0 CE D:LYS270 4.5 23.4 1.0 CG D:GLU272 4.5 26.1 1.0 CA D:ASP296 4.7 24.1 1.0 CB D:GLU272 4.8 25.8 1.0 CE1 D:PHE244 4.8 28.7 1.0 CB D:ALA293 4.8 26.1 1.0

S.Nandi, M.Razzaghi, D.Srivastava, M.Dey. Structural Basis For Allosteric Regulation of Pyruvate Kinase M2 By Phosphorylation and Acetylation. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32989054
DOI: 10.1074/JBC.RA120.015800