Magnesium in PDB 6wp6: Pyruvate Kinase M2 Mutant-S37E K433E

All present enzymatic activity of Pyruvate Kinase M2 Mutant-S37E K433E:
2.7.1.40;

The structure of Pyruvate Kinase M2 Mutant-S37E K433E, PDB code: 6wp6 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)	61.27 / 2.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.065, 92.924, 109.391, 90.00, 94.27, 90.00
R / Rfree (%)	21.5 / 25.4

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Mutant-S37E K433E (pdb code 6wp6). 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-S37E K433E, PDB code: 6wp6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyruvate Kinase M2 Mutant-S37E K433E


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-S37E K433E within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:42.1 occ:1.00 OD1 C:ASP296 2.0 42.7 1.0 OE1 C:GLU272 2.1 42.2 1.0 O1 C:OXL603 2.1 43.6 1.0 O C:HOH705 2.2 43.4 1.0 O C:HOH727 2.6 46.2 1.0 O2 C:OXL603 2.7 42.2 1.0 CD C:GLU272 3.0 43.8 1.0 C1 C:OXL603 3.0 43.7 1.0 CG C:ASP296 3.2 42.2 1.0 OE2 C:GLU272 3.3 45.4 1.0 C2 C:OXL603 3.3 44.1 1.0 CB C:ASP296 3.8 44.8 1.0 CZ C:PHE244 4.0 50.7 1.0 CE2 C:PHE244 4.1 51.1 1.0 NZ C:LYS270 4.1 35.2 1.0 OD2 C:ASP296 4.2 41.0 1.0 O3 C:OXL603 4.2 39.7 1.0 CG C:GLU272 4.3 43.1 1.0 O4 C:OXL603 4.5 42.5 1.0 CE1 C:PHE244 4.7 46.2 1.0 CB C:GLU272 4.7 44.3 1.0 N C:ASP296 4.7 35.6 1.0 CE C:LYS270 4.7 41.4 1.0 O C:HOH731 4.8 42.1 1.0 CD2 C:PHE244 4.8 48.7 1.0 CA C:ASP296 4.9 39.0 1.0 CB C:ALA293 4.9 37.3 1.0 OG C:SER243 4.9 45.3 1.0

Magnesium binding site 2 out of 2 in the Pyruvate Kinase M2 Mutant-S37E K433E


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-S37E K433E within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:32.6 occ:1.00 OD1 A:ASP113 2.6 35.3 1.0 OD1 A:ASN75 2.6 39.4 1.0 OG A:SER77 2.7 41.0 1.0 O A:THR114 2.8 36.5 1.0 OG A:SER243 3.6 32.3 1.0 CG A:ASN75 3.6 35.5 1.0 CG A:ASP113 3.7 31.2 1.0 C A:THR114 3.8 36.5 1.0 CB A:SER77 3.9 41.6 1.0 ND2 A:ASN75 4.0 41.6 1.0 NZ A:LYS270 4.1 28.1 1.0 NH2 A:ARG73 4.2 28.6 1.0 OE1 A:GLU118 4.3 56.2 1.0 CA A:LYS115 4.3 39.5 1.0 O A:ASP113 4.4 39.6 1.0 N A:SER77 4.4 39.0 1.0 N A:LYS115 4.4 40.0 1.0 O A:LYS115 4.5 43.7 1.0 OD2 A:ASP113 4.5 36.2 1.0 C A:ASP113 4.5 35.4 1.0 CB A:ASP113 4.6 31.5 1.0 N A:THR114 4.7 34.0 1.0 CA A:SER77 4.7 40.4 1.0 C A:LYS115 4.8 38.6 1.0 CB A:SER243 4.8 35.9 1.0 CA A:THR114 4.9 33.9 1.0 CB A:ASN75 4.9 30.3 1.0 N A:PHE76 5.0 38.5 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