Magnesium in PDB 4qg8: Crystal Structure of PKM2 Mutant 2

All present enzymatic activity of Crystal Structure of PKM2 Mutant 2:
2.7.1.40;

The structure of Crystal Structure of PKM2 Mutant 2, PDB code: 4qg8 was solved by P.Wang, C.Sun, T.Zhu, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.54 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.812, 117.377, 110.330, 90.00, 113.21, 90.00
R / Rfree (%)	21.3 / 26

The structure of Crystal Structure of PKM2 Mutant 2 also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of PKM2 Mutant 2 (pdb code 4qg8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of PKM2 Mutant 2, PDB code: 4qg8:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of PKM2 Mutant 2


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 PKM2 Mutant 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:27.4 occ:1.00 O A:HOH1273 2.0 30.0 1.0 OD1 A:ASP296 2.3 40.3 1.0 O9 A:MLI1004 2.3 19.8 0.6 C3 A:MLI1004 3.1 13.3 0.6 OE1 A:GLU272 3.1 16.1 1.0 C2 A:MLI1004 3.1 7.7 0.6 O6 A:MLI1004 3.1 9.3 0.6 CG A:ASP296 3.3 28.7 1.0 C1 A:MLI1004 3.4 9.0 0.6 O7 A:MLI1004 3.5 10.7 0.6 O A:HOH1187 3.7 31.4 1.0 CB A:ASP296 3.8 18.7 1.0 O A:HOH1209 4.0 13.1 1.0 O8 A:MLI1004 4.1 8.9 0.6 N A:ASP296 4.1 14.6 1.0 CD A:GLU272 4.3 20.4 1.0 OD2 A:ASP296 4.4 26.3 1.0 CA A:ASP296 4.6 14.6 1.0 CZ A:PHE244 4.7 22.7 1.0 OE2 A:GLU272 4.8 14.0 1.0 NZ A:LYS270 4.8 11.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of PKM2 Mutant 2


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 PKM2 Mutant 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:17.9 occ:1.00 O B:HOH1224 2.1 18.1 1.0 O8 B:MLI1003 2.1 13.3 0.6 OD2 B:ASP296 2.4 35.8 1.0 OE1 B:GLU272 2.4 12.8 1.0 O7 B:MLI1003 3.0 7.3 0.6 C3 B:MLI1003 3.0 8.7 0.6 C2 B:MLI1003 3.1 6.8 0.6 O B:HOH1313 3.2 33.2 1.0 C1 B:MLI1003 3.2 8.8 0.6 CG B:ASP296 3.5 16.0 1.0 CD B:GLU272 3.5 16.5 1.0 O B:HOH1115 3.8 8.7 1.0 O6 B:MLI1003 3.9 13.2 0.6 OE2 B:GLU272 3.9 14.6 1.0 CB B:ASP296 4.0 11.3 1.0 CZ B:PHE244 4.1 19.9 1.0 NZ B:LYS270 4.2 8.2 1.0 O9 B:MLI1003 4.2 3.7 0.6 O B:HOH1114 4.3 11.1 1.0 OD1 B:ASP296 4.5 18.7 1.0 CE1 B:PHE244 4.5 13.8 1.0 N B:ASP296 4.7 7.3 1.0 CE B:LYS270 4.7 7.5 1.0 O B:HOH1282 4.7 19.8 1.0 CE2 B:PHE244 4.8 17.1 1.0 CG B:GLU272 4.8 10.4 1.0 CB B:GLU272 4.9 13.6 1.0 CA B:ASP296 4.9 9.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of PKM2 Mutant 2


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 PKM2 Mutant 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:25.1 occ:1.00 OD2 C:ASP296 2.1 35.2 1.0 O C:HOH2149 2.3 19.2 1.0 OE1 C:GLU272 2.5 13.0 1.0 O9 C:MLI1003 2.6 9.2 0.6 O6 C:MLI1003 2.8 10.7 0.6 C3 C:MLI1003 3.0 13.2 0.6 CG C:ASP296 3.3 26.8 1.0 C1 C:MLI1003 3.3 10.2 0.6 C2 C:MLI1003 3.4 7.6 0.6 CD C:GLU272 3.6 14.5 1.0 O C:HOH2114 3.7 12.7 1.0 O8 C:MLI1003 3.8 14.5 0.6 OE2 C:GLU272 4.0 20.7 1.0 CB C:ASP296 4.1 14.9 1.0 OD1 C:ASP296 4.2 19.0 1.0 NZ C:LYS270 4.2 9.8 1.0 O C:HOH2024 4.3 17.0 1.0 CZ C:PHE244 4.3 16.7 1.0 O7 C:MLI1003 4.7 9.0 0.6 N C:ASP296 4.7 14.0 1.0 CE2 C:PHE244 4.8 14.4 1.0 CE C:LYS270 4.8 13.1 1.0 CE1 C:PHE244 4.9 20.0 1.0 CG C:GLU272 4.9 12.1 1.0

P.Wang, C.Sun, T.Zhu, Y.Xu. Structural Insight Into Mechanisms For Dynamic Regulation of PKM2 Protein Cell 2015.
ISSN: ESSN 1674-8018
PubMed: 25645022
DOI: 10.1007/S13238-015-0132-X