Magnesium in PDB 6nu1: Crystal Structure of Human PKM2 in Complex with L-Cysteine

All present enzymatic activity of Crystal Structure of Human PKM2 in Complex with L-Cysteine:
2.7.1.40;

The structure of Crystal Structure of Human PKM2 in Complex with L-Cysteine, PDB code: 6nu1 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)	24.70 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.829, 155.918, 94.136, 90.00, 103.51, 90.00
R / Rfree (%)	19.1 / 23.5

The structure of Crystal Structure of Human PKM2 in Complex with L-Cysteine also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human PKM2 in Complex with L-Cysteine (pdb code 6nu1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human PKM2 in Complex with L-Cysteine, PDB code: 6nu1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human PKM2 in Complex with L-Cysteine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human PKM2 in Complex with L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:36.6 occ:1.00 OD2 A:ASP296 1.9 41.0 1.0 O A:HOH712 2.1 33.9 1.0 O1 A:OXL604 2.1 42.6 1.0 OE1 A:GLU272 2.1 46.0 1.0 O A:HOH759 2.2 33.8 1.0 O2 A:OXL604 2.3 36.7 1.0 C1 A:OXL604 2.8 45.0 1.0 C2 A:OXL604 2.9 32.8 1.0 CG A:ASP296 3.0 38.4 1.0 CD A:GLU272 3.2 38.8 1.0 CB A:ASP296 3.5 40.0 1.0 OE2 A:GLU272 3.6 36.2 1.0 NZ A:LYS270 4.0 40.4 1.0 O3 A:OXL604 4.0 48.0 1.0 OD1 A:ASP296 4.1 50.2 1.0 O4 A:OXL604 4.1 34.9 1.0 N A:ASP296 4.3 32.7 1.0 CE2 A:PHE244 4.3 49.4 1.0 CE A:LYS270 4.4 37.6 1.0 CG A:GLU272 4.4 38.6 1.0 CA A:ASP296 4.6 36.8 1.0 O A:HOH791 4.7 43.2 1.0 CB A:ALA293 4.7 29.7 1.0 CB A:GLU272 4.8 34.3 1.0 CD2 A:PHE244 5.0 45.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human PKM2 in Complex with L-Cysteine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human PKM2 in Complex with L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:41.3 occ:1.00 OD2 B:ASP296 2.0 35.7 1.0 O B:HOH775 2.1 40.8 1.0 O4 B:OXL604 2.1 41.2 1.0 OE2 B:GLU272 2.1 47.7 1.0 O B:HOH706 2.2 41.4 1.0 O3 B:OXL604 2.4 44.3 1.0 C2 B:OXL604 2.9 40.6 1.0 C1 B:OXL604 3.0 48.3 1.0 CD B:GLU272 3.1 41.3 1.0 CG B:ASP296 3.2 42.8 1.0 OE1 B:GLU272 3.4 41.1 1.0 CB B:ASP296 3.7 39.2 1.0 O2 B:OXL604 4.1 37.0 1.0 OD1 B:ASP296 4.2 43.9 1.0 O1 B:OXL604 4.3 53.9 1.0 N B:ASP296 4.3 32.9 1.0 CE1 B:PHE244 4.3 47.9 1.0 NZ B:LYS270 4.4 39.9 1.0 CG B:GLU272 4.4 38.8 1.0 CA B:ASP296 4.6 35.3 1.0 CB B:ALA293 4.8 35.6 1.0 CE B:LYS270 4.8 36.8 1.0 CD1 B:PHE244 4.9 45.5 1.0 K B:K605 4.9 86.8 1.0 CB B:GLU272 4.9 40.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human PKM2 in Complex with L-Cysteine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human PKM2 in Complex with L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:41.7 occ:1.00 OD2 C:ASP296 2.0 32.5 1.0 O C:HOH731 2.0 35.1 1.0 OE1 C:GLU272 2.1 43.0 1.0 O C:HOH726 2.2 40.7 1.0 O4 C:OXL604 2.3 43.6 1.0 O3 C:OXL604 2.5 39.9 1.0 CG C:ASP296 3.1 38.5 1.0 C2 C:OXL604 3.1 47.3 1.0 C1 C:OXL604 3.2 42.8 1.0 CD C:GLU272 3.2 41.9 1.0 CB C:ASP296 3.5 39.0 1.0 OE2 C:GLU272 3.7 40.4 1.0 CZ C:PHE244 4.0 48.5 1.0 OD1 C:ASP296 4.2 37.6 1.0 O2 C:OXL604 4.3 45.2 1.0 N C:ASP296 4.4 34.6 1.0 CE1 C:PHE244 4.4 45.1 1.0 O1 C:OXL604 4.4 43.0 1.0 NZ C:LYS270 4.4 35.3 1.0 CG C:GLU272 4.5 39.6 1.0 CA C:ASP296 4.6 35.6 1.0 CE2 C:PHE244 4.6 51.7 1.0 CB C:GLU272 4.7 41.9 1.0 CE C:LYS270 4.8 38.1 1.0 CB C:ALA293 5.0 40.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human PKM2 in Complex with L-Cysteine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human PKM2 in Complex with L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg603 b:31.5 occ:1.00 O D:HOH774 2.0 32.0 1.0 O4 D:OXL604 2.0 30.6 1.0 OD2 D:ASP296 2.1 35.7 1.0 O D:HOH735 2.1 26.0 1.0 OE1 D:GLU272 2.3 24.7 1.0 O3 D:OXL604 2.3 28.0 1.0 C2 D:OXL604 2.8 37.5 1.0 C1 D:OXL604 2.9 30.6 1.0 CG D:ASP296 3.1 34.6 1.0 CD D:GLU272 3.4 25.1 1.0 CB D:ASP296 3.7 25.4 1.0 OE2 D:GLU272 3.8 29.6 1.0 O2 D:OXL604 4.0 39.3 1.0 NZ D:LYS270 4.1 24.6 1.0 O D:HOH875 4.1 44.6 1.0 O1 D:OXL604 4.1 31.7 1.0 OD1 D:ASP296 4.2 35.1 1.0 N D:ASP296 4.3 25.2 1.0 CZ D:PHE244 4.4 30.8 1.0 CE D:LYS270 4.6 24.7 1.0 CG D:GLU272 4.6 22.4 1.0 CA D:ASP296 4.6 26.0 1.0 O D:HOH714 4.6 33.3 1.0 CB D:ALA293 4.7 23.6 1.0 CB D:GLU272 4.8 24.1 1.0 CE1 D:PHE244 4.8 28.9 1.0 CE2 D:PHE244 4.8 38.0 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