Magnesium in PDB 6wp3: Pyruvate Kinase M2 Mutant-K433Q

All present enzymatic activity of Pyruvate Kinase M2 Mutant-K433Q:
2.7.1.40;

The structure of Pyruvate Kinase M2 Mutant-K433Q, PDB code: 6wp3 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)	47.11 / 1.84
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.378, 94.226, 109.638, 90.00, 94.80, 90.00
R / Rfree (%)	20.3 / 23

The structure of Pyruvate Kinase M2 Mutant-K433Q also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Mutant-K433Q (pdb code 6wp3). 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-K433Q, PDB code: 6wp3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyruvate Kinase M2 Mutant-K433Q


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-K433Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:21.3 occ:1.00 O2 A:OXL605 2.0 21.6 1.0 O A:HOH759 2.1 21.2 1.0 OD2 A:ASP296 2.1 22.6 1.0 O A:HOH793 2.1 22.3 1.0 OE1 A:GLU272 2.1 20.7 1.0 O1 A:OXL605 2.2 19.1 1.0 C2 A:OXL605 2.7 20.7 1.0 C1 A:OXL605 2.8 20.8 1.0 CD A:GLU272 3.1 24.8 1.0 CG A:ASP296 3.2 23.9 1.0 OE2 A:GLU272 3.5 21.4 1.0 CB A:ASP296 3.7 18.5 1.0 O4 A:OXL605 4.0 23.9 1.0 O3 A:OXL605 4.0 22.3 1.0 NZ A:LYS270 4.1 18.2 1.0 OD1 A:ASP296 4.3 26.6 1.0 CZ A:PHE244 4.3 28.7 1.0 N A:ASP296 4.3 21.2 1.0 O3 A:GOL603 4.4 28.0 1.0 C3 A:GOL603 4.4 29.3 1.0 CG A:GLU272 4.5 19.7 1.0 O A:HOH727 4.5 22.2 1.0 CE A:LYS270 4.5 16.8 1.0 CA A:ASP296 4.6 20.6 1.0 CB A:GLU272 4.7 21.1 1.0 CB A:ALA293 4.7 20.6 1.0 CE2 A:PHE244 4.7 26.8 1.0 CE1 A:PHE244 4.7 25.0 1.0

Magnesium binding site 2 out of 2 in the Pyruvate Kinase M2 Mutant-K433Q


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-K433Q within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:26.4 occ:1.00 O B:HOH740 2.0 26.6 1.0 OE1 B:GLU272 2.0 31.8 1.0 OD2 B:ASP296 2.1 28.0 1.0 O2 B:OXL604 2.1 30.8 1.0 O1 B:OXL604 2.1 26.0 1.0 O B:HOH755 2.2 26.3 1.0 C2 B:OXL604 2.8 30.7 1.0 C1 B:OXL604 2.8 28.8 1.0 CG B:ASP296 3.1 28.6 1.0 CD B:GLU272 3.1 28.9 1.0 OE2 B:GLU272 3.5 32.1 1.0 CB B:ASP296 3.6 23.9 1.0 O3 B:OXL604 4.1 26.1 1.0 O4 B:OXL604 4.1 31.3 1.0 N B:ASP296 4.2 24.1 1.0 NZ B:LYS270 4.2 23.7 1.0 OD1 B:ASP296 4.2 30.0 1.0 O B:HOH853 4.4 32.1 1.0 CE2 B:PHE244 4.4 35.5 1.0 CG B:GLU272 4.4 28.6 1.0 CE B:LYS270 4.5 24.5 1.0 CA B:ASP296 4.5 24.8 1.0 CB B:GLU272 4.7 26.2 1.0 CB B:ALA293 4.8 24.0 1.0 CZ B:PHE244 5.0 28.3 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