Magnesium in PDB 6nub: Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Serine

All present enzymatic activity of Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Serine:
2.7.1.40;

The structure of Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Serine, PDB code: 6nub was solved by D.Srivastava, S.Nandi, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.81 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.110, 94.230, 109.130, 90.00, 95.63, 90.00
R / Rfree (%)	15.4 / 17.4

The structure of Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Serine also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Serine (pdb code 6nub). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Serine, PDB code: 6nub:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Serine


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 - S437Y in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:10.4 occ:1.00 OE1 A:GLU272 2.0 10.7 1.0 O1 A:OXL603 2.0 12.8 1.0 O A:HOH881 2.1 12.5 1.0 OD2 A:ASP296 2.1 11.9 1.0 O A:HOH774 2.1 10.3 1.0 O2 A:OXL603 2.2 9.0 1.0 C1 A:OXL603 2.8 12.4 1.0 C2 A:OXL603 2.9 10.7 1.0 CD A:GLU272 3.1 12.3 1.0 CG A:ASP296 3.2 13.2 1.0 OE2 A:GLU272 3.5 10.1 1.0 CB A:ASP296 3.7 8.5 1.0 O3 A:OXL603 4.0 15.2 1.0 O A:HOH1060 4.1 15.6 1.0 O4 A:OXL603 4.1 10.4 1.0 NZ A:LYS270 4.2 8.3 1.0 O A:HOH783 4.2 15.7 1.0 N A:ASP296 4.2 7.3 1.0 CZ A:PHE244 4.2 14.6 1.0 O A:HOH1132 4.2 23.8 1.0 OD1 A:ASP296 4.3 15.4 1.0 O A:HOH1038 4.3 22.1 1.0 CG A:GLU272 4.4 10.5 1.0 O A:HOH886 4.5 9.9 1.0 CE A:LYS270 4.6 7.4 1.0 CA A:ASP296 4.6 8.4 1.0 CE1 A:PHE244 4.6 16.0 1.0 CB A:GLU272 4.7 13.5 1.0 CE2 A:PHE244 4.8 15.1 1.0 CB A:ALA293 4.8 10.3 1.0

Magnesium binding site 2 out of 2 in the Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Serine


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 - S437Y in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:10.3 occ:1.00 O B:HOH872 2.1 10.7 1.0 O2 B:OXL603 2.1 10.9 1.0 OD2 B:ASP296 2.1 11.3 1.0 OE1 B:GLU272 2.1 8.3 1.0 O B:HOH800 2.1 8.9 1.0 O1 B:OXL603 2.1 10.0 1.0 C2 B:OXL603 2.9 11.4 1.0 C1 B:OXL603 2.9 9.3 1.0 CD B:GLU272 3.1 11.4 1.0 CG B:ASP296 3.2 11.0 1.0 OE2 B:GLU272 3.5 9.7 1.0 CB B:ASP296 3.6 8.3 1.0 O4 B:OXL603 4.1 12.8 1.0 O3 B:OXL603 4.1 11.6 1.0 O B:HOH1092 4.1 12.8 1.0 O B:HOH911 4.2 15.2 1.0 NZ B:LYS270 4.2 9.5 1.0 O B:HOH1000 4.2 21.1 1.0 OD1 B:ASP296 4.2 14.3 1.0 N B:ASP296 4.3 9.6 1.0 CZ B:PHE244 4.3 16.7 1.0 O B:HOH1150 4.3 23.4 1.0 CG B:GLU272 4.5 10.7 1.0 CE1 B:PHE244 4.5 16.1 1.0 O B:HOH767 4.5 12.0 1.0 CE B:LYS270 4.5 7.4 1.0 CA B:ASP296 4.6 9.1 1.0 CB B:GLU272 4.7 15.1 1.0 CB B:ALA293 4.8 8.0 1.0 CE2 B:PHE244 4.9 17.6 1.0

D.Srivastava, S.Nandi, M.Dey. Mechanistic and Structural Insights Into Cysteine-Mediated Inhibition of Pyruvate Kinase Muscle Isoform 2. Biochemistry V. 58 3669 2019.
ISSN: ISSN 0006-2960
PubMed: 31386812
DOI: 10.1021/ACS.BIOCHEM.9B00349