Potassium 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:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Potassium atom in the Pyruvate Kinase M2 Mutant-S37E (pdb code 6wp4). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Pyruvate Kinase M2 Mutant-S37E, PDB code: 6wp4:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Pyruvate Kinase M2 Mutant-S37E


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-S37E within 5.0Å range: probe atom residue distance (Å) B Occ A:K605 b:21.8 occ:1.00 OD1 A:ASP113 2.7 20.7 1.0 O A:THR114 2.7 20.7 1.0 OD1 A:ASN75 2.8 22.5 1.0 OG A:SER77 2.8 20.3 1.0 O A:HOH783 2.8 20.6 1.0 CG A:ASP113 3.7 20.5 1.0 C A:THR114 3.7 19.8 1.0 OG A:SER243 3.7 20.7 1.0 CB A:SER77 3.8 22.1 1.0 CG A:ASN75 3.9 20.8 1.0 O A:ASP113 3.9 17.6 1.0 NZ A:LYS270 4.0 21.8 1.0 N A:SER77 4.0 19.2 1.0 CA A:LYS115 4.1 19.1 1.0 NH2 A:ARG73 4.2 23.7 1.0 N A:LYS115 4.2 21.4 1.0 C A:ASP113 4.3 21.4 1.0 OE1 A:GLU118 4.3 27.5 1.0 OD2 A:ASP113 4.4 19.7 1.0 CB A:ASP113 4.4 17.6 1.0 CA A:SER77 4.4 18.9 1.0 O A:HOH787 4.5 22.4 1.0 ND2 A:ASN75 4.5 22.4 1.0 O A:LYS115 4.5 20.9 1.0 N A:THR114 4.6 18.1 1.0 N A:PHE76 4.7 19.6 1.0 C A:LYS115 4.7 21.2 1.0 CA A:THR114 4.8 19.0 1.0 CB A:SER243 4.9 20.3 1.0 CB A:ASN75 4.9 18.3 1.0 CA A:ASN75 5.0 19.5 1.0 CA A:ASP113 5.0 17.7 1.0 C A:PHE76 5.0 21.5 1.0

Potassium binding site 2 out of 5 in the Pyruvate Kinase M2 Mutant-S37E


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-S37E within 5.0Å range: probe atom residue distance (Å) B Occ B:K605 b:24.0 occ:1.00 OD1 B:ASP113 2.7 24.6 1.0 OD1 B:ASN75 2.7 21.3 1.0 O B:THR114 2.7 23.0 1.0 OG B:SER77 2.8 22.6 1.0 O B:HOH822 2.8 31.1 1.0 O B:HOH764 2.8 23.2 1.0 C B:THR114 3.7 23.4 1.0 CG B:ASP113 3.7 24.1 1.0 OG B:SER243 3.8 23.5 1.0 CG B:ASN75 3.8 20.3 1.0 O B:ASP113 3.8 20.7 1.0 CB B:SER77 3.8 20.0 1.0 N B:SER77 4.0 17.5 1.0 NZ B:LYS270 4.0 21.6 1.0 CA B:LYS115 4.1 21.9 1.0 NH2 B:ARG73 4.1 23.8 1.0 C B:ASP113 4.2 22.5 1.0 N B:LYS115 4.2 22.5 1.0 OE1 B:GLU118 4.3 26.3 1.0 ND2 B:ASN75 4.4 23.8 1.0 CA B:SER77 4.4 20.6 1.0 CB B:ASP113 4.4 20.6 1.0 O B:LYS115 4.4 23.3 1.0 OD2 B:ASP113 4.5 26.6 1.0 O B:HOH729 4.6 20.5 1.0 N B:THR114 4.6 18.4 1.0 C B:LYS115 4.7 22.6 1.0 N B:PHE76 4.7 19.4 1.0 CA B:THR114 4.8 22.4 1.0 CB B:SER243 4.9 21.6 1.0 CB B:ASN75 4.9 18.0 1.0 CA B:ASN75 4.9 19.9 1.0 C B:PHE76 4.9 22.6 1.0 CA B:ASP113 5.0 22.4 1.0

Potassium binding site 3 out of 5 in the Pyruvate Kinase M2 Mutant-S37E


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Pyruvate Kinase M2 Mutant-S37E within 5.0Å range: probe atom residue distance (Å) B Occ C:K604 b:28.6 occ:1.00 O C:THR114 2.7 23.0 1.0 OD1 C:ASP113 2.7 27.1 1.0 OD1 C:ASN75 2.8 24.9 1.0 OG C:SER77 2.8 27.2 1.0 O C:HOH819 2.9 30.4 1.0 O C:HOH743 3.0 24.8 1.0 C C:THR114 3.6 26.7 1.0 OG C:SER243 3.6 23.7 1.0 CG C:ASP113 3.8 28.3 1.0 CG C:ASN75 3.8 27.0 1.0 O C:ASP113 3.9 26.3 1.0 CB C:SER77 3.9 29.1 1.0 NZ C:LYS270 4.0 22.2 1.0 CA C:LYS115 4.1 27.3 1.0 N C:SER77 4.1 26.9 1.0 N C:LYS115 4.2 25.6 1.0 C C:ASP113 4.2 25.4 1.0 NH2 C:ARG73 4.3 26.9 1.0 O1 C:GOL606 4.3 39.7 1.0 O C:LYS115 4.4 26.9 1.0 ND2 C:ASN75 4.4 26.3 1.0 OE1 C:GLU118 4.4 33.3 1.0 N C:THR114 4.5 22.7 1.0 CB C:ASP113 4.6 22.1 1.0 CA C:SER77 4.6 28.5 1.0 C C:LYS115 4.6 26.0 1.0 OD2 C:ASP113 4.6 28.3 1.0 CA C:THR114 4.7 26.2 1.0 N C:PHE76 4.7 27.1 1.0 CB C:SER243 4.7 24.0 1.0 CB C:ASN75 4.9 21.9 1.0 CA C:ASN75 4.9 28.6 1.0

Potassium binding site 4 out of 5 in the Pyruvate Kinase M2 Mutant-S37E


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Pyruvate Kinase M2 Mutant-S37E within 5.0Å range: probe atom residue distance (Å) B Occ D:K605 b:28.1 occ:1.00 OD1 D:ASP113 2.6 27.5 1.0 OD1 D:ASN75 2.7 28.9 1.0 O D:THR114 2.7 24.1 1.0 OG D:SER77 2.9 31.0 1.0 O D:HOH719 2.9 26.3 1.0 C D:THR114 3.6 27.7 1.0 OG D:SER243 3.6 22.5 1.0 CG D:ASP113 3.7 27.6 1.0 O D:ASP113 3.7 26.3 1.0 CG D:ASN75 3.7 27.3 1.0 CB D:SER77 3.8 32.7 1.0 NZ D:LYS270 3.9 24.6 1.0 N D:SER77 4.0 30.5 1.0 CA D:LYS115 4.1 28.1 1.0 C D:ASP113 4.1 27.4 1.0 N D:LYS115 4.2 28.4 1.0 NH2 D:ARG73 4.2 31.6 1.0 CB D:ASP113 4.3 25.3 1.0 ND2 D:ASN75 4.3 34.4 1.0 O D:LYS115 4.4 30.1 1.0 CA D:SER77 4.5 31.1 1.0 O D:HOH757 4.5 27.2 1.0 OD2 D:ASP113 4.5 30.8 1.0 N D:THR114 4.5 27.4 1.0 C D:LYS115 4.6 27.4 1.0 OE1 D:GLU118 4.6 33.7 1.0 N D:PHE76 4.7 26.1 1.0 CA D:THR114 4.7 26.9 1.0 CB D:SER243 4.8 26.8 1.0 CB D:ASN75 4.8 27.2 1.0 CA D:ASP113 4.9 24.0 1.0 CA D:ASN75 4.9 25.9 1.0 C D:PHE76 4.9 30.9 1.0 C D:ASN75 5.0 29.6 1.0

Potassium binding site 5 out of 5 in the Pyruvate Kinase M2 Mutant-S37E


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Pyruvate Kinase M2 Mutant-S37E within 5.0Å range: probe atom residue distance (Å) B Occ D:K606 b:73.6 occ:1.00 OD2 D:ASP236 3.4 38.1 1.0 NH2 D:ARG461 3.8 26.8 1.0 CG D:ASP236 4.3 34.8 1.0 OD1 D:ASP236 4.3 38.6 1.0 CB D:GLN458 4.5 28.9 1.0 N D:GLN458 4.7 25.5 1.0 CZ D:ARG461 4.9 28.0 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