Magnesium in PDB 6b6u: Pyruvate Kinase M2 Mutant - S437Y

All present enzymatic activity of Pyruvate Kinase M2 Mutant - S437Y:
2.7.1.40;

The structure of Pyruvate Kinase M2 Mutant - S437Y, PDB code: 6b6u was solved by D.Srivastava, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.99 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.350, 93.610, 109.360, 90.00, 95.64, 90.00
R / Rfree (%)	13 / 14.9

The structure of Pyruvate Kinase M2 Mutant - S437Y also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Mutant - S437Y (pdb code 6b6u). 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 - S437Y, PDB code: 6b6u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyruvate Kinase M2 Mutant - S437Y


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 - S437Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:9.8 occ:1.00 O A:HOH785 2.0 8.6 1.0 OE1 A:GLU272 2.1 9.4 1.0 OD2 A:ASP296 2.1 10.6 1.0 O1 A:OXL602 2.1 10.2 1.0 O A:HOH926 2.1 10.2 1.0 O2 A:OXL602 2.1 9.9 1.0 C1 A:OXL602 2.9 11.6 1.0 C2 A:OXL602 2.9 9.6 1.0 HB2 A:ASP296 3.1 12.3 1.0 CD A:GLU272 3.1 9.2 1.0 CG A:ASP296 3.2 11.4 1.0 HZ1 A:LYS270 3.4 11.1 1.0 H A:ASP296 3.5 10.5 1.0 OE2 A:GLU272 3.5 9.2 1.0 CB A:ASP296 3.6 10.3 1.0 HB1 A:ALA293 3.9 10.4 1.0 HZ A:PHE244 4.0 18.0 1.0 O A:HOH1057 4.1 13.1 1.0 HE2 A:LYS270 4.1 9.8 1.0 O4 A:OXL602 4.1 10.3 1.0 O3 A:OXL602 4.1 13.5 1.0 NZ A:LYS270 4.1 9.2 1.0 O A:HOH882 4.2 11.6 1.0 N A:ASP296 4.2 8.8 1.0 CZ A:PHE244 4.2 15.0 1.0 OD1 A:ASP296 4.3 14.3 1.0 HZ3 A:LYS270 4.3 11.1 1.0 HB2 A:GLU272 4.3 14.6 1.0 O A:HOH1135 4.3 23.6 1.0 HB3 A:ASP296 4.3 12.3 1.0 O A:HOH1058 4.3 20.4 1.0 CG A:GLU272 4.4 10.4 1.0 HB3 A:GLU272 4.5 14.6 1.0 O A:HOH878 4.5 7.9 1.0 HE1 A:PHE244 4.6 17.7 1.0 CE A:LYS270 4.6 8.1 1.0 CA A:ASP296 4.6 9.1 1.0 CE1 A:PHE244 4.6 14.7 1.0 CB A:GLU272 4.7 12.2 1.0 HE3 A:LYS270 4.7 9.8 1.0 CB A:ALA293 4.8 8.6 1.0 CE2 A:PHE244 4.8 15.9 1.0 HZ2 A:LYS270 4.8 11.1 1.0 HB3 A:ALA293 4.9 10.4 1.0 HG3 A:GLU272 4.9 12.5 1.0 HB3 A:SER243 4.9 10.1 1.0 HE2 A:PHE244 5.0 19.1 1.0

Magnesium binding site 2 out of 2 in the Pyruvate Kinase M2 Mutant - S437Y


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 - S437Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:9.6 occ:1.00 OE1 B:GLU272 2.0 9.8 1.0 OD2 B:ASP296 2.1 9.5 1.0 O B:HOH805 2.1 7.8 1.0 O B:HOH907 2.1 8.8 1.0 O2 B:OXL602 2.1 10.0 1.0 O1 B:OXL602 2.1 9.3 1.0 C2 B:OXL602 2.8 11.3 1.0 C1 B:OXL602 2.9 9.9 1.0 CD B:GLU272 3.1 10.2 1.0 CG B:ASP296 3.2 9.8 1.0 HB2 B:ASP296 3.2 10.9 1.0 HZ1 B:LYS270 3.4 11.0 1.0 OE2 B:GLU272 3.5 9.5 1.0 H B:ASP296 3.5 10.3 1.0 CB B:ASP296 3.7 9.1 1.0 HB1 B:ALA293 3.9 11.6 1.0 HZ B:PHE244 4.0 17.9 1.0 HE2 B:LYS270 4.1 8.9 1.0 O4 B:OXL602 4.1 12.9 1.0 O3 B:OXL602 4.1 10.6 1.0 O B:HOH1098 4.1 13.4 1.0 O B:HOH894 4.2 12.5 1.0 NZ B:LYS270 4.2 9.2 1.0 HB3 B:GLU272 4.2 17.8 1.0 OD1 B:ASP296 4.2 12.3 1.0 CZ B:PHE244 4.2 14.9 1.0 N B:ASP296 4.3 8.6 1.0 O B:HOH1165 4.3 19.5 1.0 O B:HOH1076 4.3 17.4 1.0 HZ3 B:LYS270 4.3 11.0 1.0 HB3 B:ASP296 4.4 10.9 1.0 CG B:GLU272 4.4 10.6 1.0 HE1 B:PHE244 4.4 17.2 1.0 CE1 B:PHE244 4.5 14.3 1.0 CE B:LYS270 4.5 7.4 1.0 O B:HOH902 4.5 7.9 1.0 CA B:ASP296 4.6 8.5 1.0 HG2 B:GLU272 4.7 12.7 1.0 HE3 B:LYS270 4.7 8.9 1.0 CB B:ALA293 4.8 9.7 1.0 CB B:GLU272 4.8 14.8 1.0 HZ2 B:LYS270 4.9 11.0 1.0 CE2 B:PHE244 4.9 14.3 1.0 HB3 B:ALA293 4.9 11.6 1.0 HB3 B:SER243 5.0 11.2 1.0

D.Srivastava, M.Razzaghi, M.T.Henzl, M.Dey. Structural Investigation of A Dimeric Variant of Pyruvate Kinase Muscle Isoform 2. Biochemistry V. 56 6517 2017.
ISSN: ISSN 1520-4995
PubMed: 29182273
DOI: 10.1021/ACS.BIOCHEM.7B01013