Potassium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium where determined in the Pyruvate Kinase M2 Mutant - S437Y in Complex with L-Serine, PDB code: 6nub:
Jump to Potassium binding site number: 1; 2;

Potassium 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 Potassium with other atoms in the K 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:K604 b:10.8 occ:1.00 OD1 A:ASP113 2.7 12.5 1.0 O A:THR114 2.7 9.3 1.0 OG A:SER77 2.7 10.8 1.0 O A:HOH886 2.8 9.9 1.0 OD1 A:ASN75 2.8 11.2 1.0 O A:HOH1060 2.8 15.6 1.0 OG A:SER243 3.6 9.0 1.0 C A:THR114 3.7 10.0 1.0 CG A:ASP113 3.7 11.3 1.0 CG A:ASN75 3.8 11.5 1.0 CB A:SER77 3.8 10.3 1.0 NZ A:LYS270 3.9 8.3 1.0 O A:ASP113 4.0 9.2 1.0 N A:SER77 4.1 8.3 1.0 CA A:LYS115 4.2 9.1 1.0 N A:LYS115 4.3 8.8 1.0 O A:HOH1015 4.3 25.9 1.0 NH2 A:ARG73 4.3 12.8 1.0 C A:ASP113 4.3 9.7 1.0 OE2 A:GLU118 4.4 12.9 1.0 ND2 A:ASN75 4.4 15.0 1.0 O A:LYS115 4.4 11.0 1.0 O A:HOH774 4.4 10.3 1.0 CA A:SER77 4.5 10.8 1.0 CB A:ASP113 4.5 8.9 1.0 OD2 A:ASP113 4.5 8.5 1.0 N A:THR114 4.6 8.2 1.0 N A:PHE76 4.7 8.6 1.0 C A:LYS115 4.7 11.8 1.0 CA A:THR114 4.8 8.2 1.0 CB A:SER243 4.8 7.4 1.0 CB A:ASN75 4.9 11.1 1.0 CA A:ASN75 4.9 9.8 1.0

Potassium 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 Potassium with other atoms in the K 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:K604 b:11.4 occ:1.00 OD1 B:ASP113 2.7 11.5 1.0 O B:THR114 2.7 10.7 1.0 OD1 B:ASN75 2.7 11.3 1.0 OG B:SER77 2.8 12.8 1.0 O B:HOH1092 2.8 12.8 1.0 O B:HOH767 2.8 12.0 1.0 C B:THR114 3.6 11.1 1.0 OG B:SER243 3.7 9.4 1.0 CG B:ASN75 3.7 13.3 1.0 CG B:ASP113 3.8 10.3 1.0 CB B:SER77 3.9 12.0 1.0 O B:ASP113 3.9 10.2 1.0 NZ B:LYS270 4.0 9.5 1.0 N B:SER77 4.1 9.8 1.0 CA B:LYS115 4.1 11.9 1.0 N B:LYS115 4.2 8.8 1.0 C B:ASP113 4.3 10.2 1.0 ND2 B:ASN75 4.3 15.5 1.0 OE2 B:GLU118 4.3 16.2 1.0 NH2 B:ARG73 4.3 15.0 1.0 O B:LYS115 4.4 13.7 1.0 O B:HOH800 4.5 8.9 1.0 CB B:ASP113 4.6 8.2 1.0 CA B:SER77 4.6 14.5 1.0 OD2 B:ASP113 4.6 11.0 1.0 N B:THR114 4.6 9.4 1.0 C B:LYS115 4.7 12.5 1.0 N B:PHE76 4.7 10.5 1.0 CA B:THR114 4.7 10.2 1.0 CB B:SER243 4.8 8.9 1.0 CB B:ASN75 4.9 12.1 1.0 CA B:ASN75 4.9 9.5 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