Magnesium in PDB 6v75: Crystal Structure of Human PKM2 in Complex with L-Aspartate

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

The structure of Crystal Structure of Human PKM2 in Complex with L-Aspartate, PDB code: 6v75 was solved by S.Nandi, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.52 / 2.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.523, 157.955, 93.031, 90.00, 101.08, 90.00
R / Rfree (%)	24.6 / 28.4

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

Potassium	(K)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Human PKM2 in Complex with L-Aspartate (pdb code 6v75). 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-Aspartate, PDB code: 6v75:
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-Aspartate


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-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg608 b:57.4 occ:1.00 OE1 C:GLU272 2.1 53.8 1.0 O1 C:OXL609 2.3 55.3 1.0 OD2 C:ASP296 2.3 60.2 1.0 O2 C:OXL609 2.7 64.6 1.0 C1 C:OXL609 3.2 62.2 1.0 CD C:GLU272 3.3 54.1 1.0 C2 C:OXL609 3.4 64.6 1.0 CG C:ASP296 3.5 60.0 1.0 NZ C:LYS270 3.9 44.6 1.0 OE2 C:GLU272 3.9 53.9 1.0 CB C:ASP296 4.0 63.4 1.0 CZ C:PHE244 4.0 57.4 1.0 CE2 C:PHE244 4.2 57.5 1.0 O3 C:OXL609 4.4 57.9 1.0 CG C:GLU272 4.4 52.6 1.0 OD1 C:ASP296 4.5 58.3 1.0 CE C:LYS270 4.5 50.0 1.0 O4 C:OXL609 4.6 61.1 1.0 CE1 C:PHE244 4.8 58.6 1.0 OE2 C:GLU118 4.9 66.7 1.0 N C:ASP296 4.9 60.4 1.0 K C:K601 5.0 65.8 1.0

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


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-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:60.2 occ:1.00 OE1 A:GLU272 2.7 73.9 1.0 OD2 A:ASP296 2.9 69.4 1.0 CD A:GLU272 3.7 70.2 1.0 CB A:ALA293 3.8 62.7 1.0 CG A:ASP296 3.9 72.2 1.0 N A:ASP296 4.1 65.4 1.0 CB A:ASP296 4.4 64.2 1.0 OE2 A:GLU272 4.5 60.8 1.0 CG A:GLU272 4.6 68.2 1.0 CA A:GLY295 4.7 59.2 1.0 CG2 A:THR328 4.7 55.0 1.0 O A:ALA293 4.7 62.9 1.0 N A:GLY295 4.8 62.9 1.0 CA A:ALA293 4.8 60.4 1.0 CA A:ASP296 4.9 63.1 1.0 C A:ALA293 4.9 65.1 1.0 C A:GLY295 4.9 60.5 1.0 OD1 A:ASP296 4.9 64.9 1.0

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


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-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg609 b:59.7 occ:1.00 OD1 B:ASP296 2.1 67.5 1.0 OE1 B:GLU272 3.1 74.1 1.0 CG B:ASP296 3.4 76.0 1.0 OD2 B:ASP296 4.0 84.0 1.0 CB B:ALA293 4.0 56.5 1.0 CD B:GLU272 4.1 68.0 1.0 NZ B:LYS270 4.1 58.1 1.0 N B:ASP296 4.1 53.9 1.0 CE B:LYS270 4.5 62.1 1.0 CB B:ASP296 4.5 66.8 1.0 CG2 B:THR328 4.5 61.2 1.0 CA B:GLY295 4.7 63.9 1.0 CG B:GLU272 4.7 58.4 1.0 N B:GLY295 4.9 69.4 1.0 C B:GLY295 4.9 55.3 1.0 CA B:ASP296 5.0 60.2 1.0

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


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-Aspartate within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg606 b:58.7 occ:1.00 OE1 D:GLU272 2.6 77.8 1.0 CB D:ASP296 2.9 75.7 1.0 N D:ASP296 3.6 71.4 1.0 CG D:ASP296 3.7 76.0 1.0 CD D:GLU272 3.8 72.5 1.0 CA D:ASP296 3.8 75.3 1.0 OD1 D:ASP296 3.8 74.2 1.0 CB D:ALA293 4.1 68.0 1.0 CG D:GLU272 4.2 67.7 1.0 OD2 D:ASP296 4.6 84.0 1.0 NZ D:LYS270 4.7 63.5 1.0 C D:GLY295 4.8 67.8 1.0 OE2 D:GLU272 4.8 71.0 1.0 CG2 D:THR328 4.9 65.2 1.0

S.Nandi, M.Dey. Biochemical and Structural Investigation of Pyurvate Kinase Muscle Isoform 2 Regulation By Amino Acids To Be Published.