Potassium 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:

Magnesium

(Mg)

3 atoms

The binding sites of Potassium atom in the Pyruvate Kinase M2 Mutant-S37D (pdb code 6wp5). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Pyruvate Kinase M2 Mutant-S37D, PDB code: 6wp5:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Pyruvate Kinase M2 Mutant-S37D


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-S37D within 5.0Å range: probe atom residue distance (Å) B Occ B:K601 b:41.9 occ:1.00 O B:HOH762 3.1 40.5 1.0 CG2 B:THR50 3.7 24.1 1.0 NH1 B:ARG73 3.7 26.2 1.0 ND2 B:ASN75 3.7 33.4 1.0 C B:SER362 4.1 30.2 1.0 CB B:SER362 4.1 28.1 1.0 N B:GLY363 4.2 29.3 1.0 CA B:SER362 4.3 30.1 1.0 O B:SER362 4.3 31.5 1.0 CB B:ALA366 4.4 31.6 1.0 CB B:THR50 4.5 30.3 1.0 OG1 B:THR50 4.6 27.3 1.0 OG B:SER362 4.7 31.7 1.0 CB B:ASN75 4.7 26.8 1.0 CG B:ASN75 4.7 33.4 1.0 CZ B:ARG73 4.7 30.1 1.0 CA B:GLY363 4.8 31.7 1.0 NH2 B:ARG73 4.8 27.2 1.0

Potassium binding site 2 out of 4 in the Pyruvate Kinase M2 Mutant-S37D


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-S37D within 5.0Å range: probe atom residue distance (Å) B Occ B:K602 b:59.1 occ:1.00 OD1 B:ASP113 2.9 38.4 1.0 O B:THR114 3.0 37.3 1.0 OG B:SER77 3.0 42.2 1.0 OD1 B:ASN75 3.1 37.2 1.0 NZ B:LYS270 3.4 31.0 1.0 OG B:SER243 3.5 29.7 1.0 CG B:ASP113 3.9 35.9 1.0 CG B:ASN75 3.9 33.4 1.0 OE2 B:GLU118 4.0 44.5 1.0 C B:THR114 4.1 36.4 1.0 CB B:SER77 4.1 36.6 1.0 NH2 B:ARG73 4.2 27.2 1.0 ND2 B:ASN75 4.2 33.4 1.0 O B:HOH701 4.2 29.3 1.0 OD2 B:ASP113 4.3 32.0 1.0 O B:LYS115 4.4 35.7 1.0 CA B:LYS115 4.5 38.4 1.0 O B:ASP113 4.5 36.5 1.0 O B:HOH716 4.6 32.0 1.0 O2 B:OXL606 4.6 35.5 1.0 CB B:SER243 4.7 30.1 1.0 N B:LYS115 4.7 34.5 1.0 N B:SER77 4.7 37.2 1.0 C B:ASP113 4.8 33.4 1.0 C B:LYS115 4.8 37.9 1.0 CE B:LYS270 4.9 29.3 1.0 CB B:ASP113 4.9 29.3 1.0 CA B:SER77 4.9 38.0 1.0

Potassium binding site 3 out of 4 in the Pyruvate Kinase M2 Mutant-S37D


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-S37D within 5.0Å range: probe atom residue distance (Å) B Occ A:K601 b:67.6 occ:1.00 O A:HOH729 3.1 34.1 1.0 O A:HOH711 3.2 28.8 1.0 O4 A:OXL607 3.2 36.2 1.0 NZ A:LYS270 3.4 33.3 1.0 OG A:SER77 3.6 45.4 1.0 OD1 A:ASN75 3.7 44.5 1.0 OD1 A:ASP113 3.8 33.4 1.0 NH2 A:ARG73 3.8 30.2 1.0 ND2 A:ASN75 3.8 41.5 1.0 OE2 A:GLU118 4.0 47.5 1.0 CG A:ASN75 4.1 40.6 1.0 MG A:MG606 4.2 36.4 1.0 OG A:SER243 4.2 30.5 1.0 C2 A:OXL607 4.2 35.0 1.0 O A:THR114 4.4 33.9 1.0 CG A:ASP113 4.6 34.5 1.0 CB A:SER77 4.6 41.0 1.0 O2 A:OXL607 4.7 37.2 1.0 OD2 A:ASP113 4.8 30.1 1.0 CE A:LYS270 4.9 32.0 1.0

Potassium binding site 4 out of 4 in the Pyruvate Kinase M2 Mutant-S37D


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-S37D within 5.0Å range: probe atom residue distance (Å) B Occ C:K601 b:77.2 occ:1.00 OG C:SER77 2.9 53.5 1.0 O C:THR114 3.2 52.1 1.0 OD1 C:ASP113 3.2 49.1 1.0 OD1 C:ASN75 3.2 43.4 1.0 OG C:SER243 3.4 41.3 1.0 OE2 C:GLU118 3.7 64.0 1.0 NZ C:LYS270 3.7 43.3 1.0 O C:LYS115 4.0 53.8 1.0 CB C:SER77 4.1 54.6 1.0 CG C:ASP113 4.1 45.8 1.0 CG C:ASN75 4.1 45.1 1.0 C C:THR114 4.3 55.0 1.0 ND2 C:ASN75 4.3 51.0 1.0 O4 C:OXL605 4.3 46.4 1.0 CA C:LYS115 4.5 54.8 1.0 NH2 C:ARG73 4.6 42.0 1.0 OD2 C:ASP113 4.6 45.4 1.0 MG C:MG604 4.6 49.7 1.0 CB C:SER243 4.6 45.0 1.0 C C:LYS115 4.7 52.9 1.0 CD C:GLU118 4.7 60.9 1.0 O C:ASP113 4.7 49.9 1.0 N C:SER77 4.8 51.4 1.0 N C:LYS115 4.9 52.4 1.0 CA C:SER77 4.9 53.7 1.0 CE C:LYS270 4.9 37.1 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