Magnesium in PDB 6nu5: Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Cysteine

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

The structure of Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Cysteine, PDB code: 6nu5 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)	41.98 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.000, 94.130, 109.260, 90.00, 95.61, 90.00
R / Rfree (%)	16.6 / 18.2

The structure of Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Cysteine 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-Cysteine (pdb code 6nu5). 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-Cysteine, PDB code: 6nu5:
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-Cysteine


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-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:11.7 occ:1.00 OE1 A:GLU272 2.0 12.8 1.0 O A:HOH784 2.0 12.9 1.0 O1 A:OXL602 2.1 14.6 1.0 OD2 A:ASP296 2.1 12.8 1.0 O A:HOH844 2.1 13.8 1.0 O2 A:OXL602 2.1 9.8 1.0 C1 A:OXL602 2.8 16.5 1.0 C2 A:OXL602 2.8 11.8 1.0 CD A:GLU272 3.1 11.8 1.0 CG A:ASP296 3.2 13.8 1.0 OE2 A:GLU272 3.5 11.9 1.0 CB A:ASP296 3.7 9.9 1.0 O A:HOH1055 4.0 18.2 1.0 O3 A:OXL602 4.1 17.1 1.0 O4 A:OXL602 4.1 12.1 1.0 NZ A:LYS270 4.2 10.1 1.0 O A:HOH796 4.2 17.6 1.0 O A:HOH1120 4.2 24.9 1.0 N A:ASP296 4.2 9.5 1.0 OD1 A:ASP296 4.3 16.5 1.0 CZ A:PHE244 4.3 16.9 1.0 O A:HOH1044 4.3 22.8 1.0 CG A:GLU272 4.4 10.3 1.0 O A:HOH904 4.5 11.7 1.0 CE A:LYS270 4.6 7.7 1.0 CA A:ASP296 4.6 11.3 1.0 CE1 A:PHE244 4.7 16.6 1.0 CB A:GLU272 4.7 15.2 1.0 CE2 A:PHE244 4.7 17.2 1.0 CB A:ALA293 4.8 11.2 1.0

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


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-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg607 b:11.3 occ:1.00 OE1 B:GLU272 2.0 10.5 1.0 OD2 B:ASP296 2.1 12.7 1.0 O B:HOH884 2.1 11.7 1.0 O2 B:OXL602 2.1 13.0 1.0 O B:HOH827 2.1 11.3 1.0 O1 B:OXL602 2.1 11.4 1.0 C2 B:OXL602 2.9 12.3 1.0 C1 B:OXL602 2.9 10.0 1.0 CD B:GLU272 3.1 13.0 1.0 CG B:ASP296 3.1 12.6 1.0 OE2 B:GLU272 3.5 11.3 1.0 CB B:ASP296 3.6 10.7 1.0 O4 B:OXL602 4.1 13.6 1.0 O3 B:OXL602 4.1 12.9 1.0 O B:HOH1078 4.1 15.8 1.0 O B:HOH903 4.2 17.1 1.0 N B:ASP296 4.2 10.8 1.0 NZ B:LYS270 4.2 9.4 1.0 O B:HOH1132 4.2 22.5 1.0 OD1 B:ASP296 4.2 16.0 1.0 O B:HOH998 4.3 21.5 1.0 CZ B:PHE244 4.3 15.3 1.0 CG B:GLU272 4.4 14.3 1.0 CE1 B:PHE244 4.5 16.5 1.0 CA B:ASP296 4.5 11.2 1.0 O B:HOH778 4.5 13.5 1.0 CE B:LYS270 4.6 7.0 1.0 CB B:GLU272 4.6 19.0 1.0 CB B:ALA293 4.8 10.5 1.0 CE2 B:PHE244 4.9 18.9 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