Magnesium in PDB 6wp5: Pyruvate Kinase M2 Mutant-S37D

All present enzymatic activity of Pyruvate Kinase M2 Mutant-S37D:
2.7.1.40;

The structure of Pyruvate Kinase M2 Mutant-S37D, PDB code: 6wp5 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)	19.84 / 2.17
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.625, 117.567, 109.965, 90.00, 112.63, 90.00
R / Rfree (%)	21.7 / 26

The structure of Pyruvate Kinase M2 Mutant-S37D also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Mutant-S37D (pdb code 6wp5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pyruvate Kinase M2 Mutant-S37D, PDB code: 6wp5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Pyruvate Kinase M2 Mutant-S37D


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-S37D within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:33.5 occ:1.00 O B:HOH701 2.0 29.3 1.0 OD2 B:ASP296 2.0 27.8 1.0 O1 B:OXL606 2.1 29.4 1.0 O2 B:OXL606 2.1 35.5 1.0 O B:HOH716 2.1 32.0 1.0 OE1 B:GLU272 2.5 35.4 1.0 C1 B:OXL606 2.8 33.2 1.0 C2 B:OXL606 2.8 36.5 1.0 CG B:ASP296 3.0 31.3 1.0 CB B:ASP296 3.4 27.4 1.0 CD B:GLU272 3.7 36.0 1.0 O3 B:OXL606 4.0 30.8 1.0 O4 B:OXL606 4.0 38.2 1.0 N B:ASP296 4.1 25.6 1.0 OD1 B:ASP296 4.1 29.1 1.0 O B:HOH753 4.2 42.0 1.0 CZ B:PHE244 4.2 42.2 1.0 NZ B:LYS270 4.3 31.0 1.0 CA B:ASP296 4.4 29.2 1.0 CG B:GLU272 4.5 34.7 1.0 OE2 B:GLU272 4.5 36.8 1.0 CE2 B:PHE244 4.6 43.1 1.0 CE B:LYS270 4.6 29.3 1.0 CB B:GLU272 4.7 33.5 1.0 CB B:ALA293 4.7 26.6 1.0 CE1 B:PHE244 4.8 40.1 1.0

Magnesium binding site 2 out of 3 in the Pyruvate Kinase M2 Mutant-S37D


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-S37D within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:36.4 occ:1.00 O A:HOH711 2.0 28.8 1.0 O3 A:OXL607 2.0 30.1 1.0 O4 A:OXL607 2.2 36.2 1.0 O A:HOH729 2.2 34.1 1.0 OE1 A:GLU272 2.2 34.5 1.0 OD2 A:ASP296 2.2 33.7 1.0 C1 A:OXL607 2.8 32.1 1.0 C2 A:OXL607 2.8 35.0 1.0 CG A:ASP296 3.3 35.4 1.0 CD A:GLU272 3.3 34.7 1.0 OE2 A:GLU272 3.6 33.1 1.0 CB A:ASP296 3.6 31.8 1.0 O1 A:OXL607 4.0 32.4 1.0 O2 A:OXL607 4.1 37.2 1.0 CZ A:PHE244 4.1 40.5 1.0 NZ A:LYS270 4.1 33.3 1.0 K A:K601 4.2 67.6 1.0 CE2 A:PHE244 4.3 43.1 1.0 N A:ASP296 4.3 29.1 1.0 OD1 A:ASP296 4.4 40.1 1.0 CE A:LYS270 4.5 32.0 1.0 CA A:ASP296 4.6 30.0 1.0 CG A:GLU272 4.6 33.2 1.0 CB A:GLU272 4.8 30.0 1.0 CB A:ALA293 4.8 29.0 1.0 CE1 A:PHE244 4.9 37.4 1.0

Magnesium binding site 3 out of 3 in the Pyruvate Kinase M2 Mutant-S37D


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-S37D within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg604 b:49.7 occ:1.00 OD2 C:ASP296 2.0 44.0 1.0 O4 C:OXL605 2.1 46.4 1.0 O3 C:OXL605 2.4 46.2 1.0 OE1 C:GLU272 2.6 43.3 1.0 C2 C:OXL605 2.9 46.5 1.0 C1 C:OXL605 3.0 47.8 1.0 CG C:ASP296 3.2 45.8 1.0 CD C:GLU272 3.6 43.7 1.0 OE2 C:GLU272 3.8 47.3 1.0 CB C:ASP296 3.9 41.6 1.0 O2 C:OXL605 4.1 43.7 1.0 CZ C:PHE244 4.1 49.2 1.0 O C:HOH715 4.1 50.1 1.0 CE2 C:PHE244 4.2 53.8 1.0 OD1 C:ASP296 4.2 48.7 1.0 O1 C:OXL605 4.3 41.8 1.0 NZ C:LYS270 4.4 43.3 1.0 N C:ASP296 4.6 40.2 1.0 K C:K601 4.6 77.2 1.0 CE C:LYS270 4.7 37.1 1.0 CA C:ASP296 4.9 41.3 1.0 CG C:GLU272 4.9 42.9 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