Magnesium in PDB 6v74: Crystal Structure of Human PKM2 in Complex with L-Asparagine

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

The structure of Crystal Structure of Human PKM2 in Complex with L-Asparagine, PDB code: 6v74 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)	58.62 / 2.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.990, 154.580, 92.150, 90.00, 102.54, 90.00
R / Rfree (%)	23.3 / 27.5

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

Potassium	(K)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human PKM2 in Complex with L-Asparagine (pdb code 6v74). 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-Asparagine, PDB code: 6v74:
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-Asparagine


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-Asparagine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:42.6 occ:1.00 O2 A:OXL605 2.1 43.1 1.0 OD2 A:ASP296 2.3 43.8 1.0 OE1 A:GLU272 2.4 46.5 1.0 O1 A:OXL605 2.7 45.4 1.0 C2 A:OXL605 3.0 42.2 1.0 CD A:GLU272 3.2 34.4 1.0 C1 A:OXL605 3.3 42.2 1.0 CG A:ASP296 3.5 40.7 1.0 OE2 A:GLU272 3.6 41.7 1.0 NZ A:LYS270 3.6 27.4 1.0 CE2 A:PHE244 3.9 50.8 1.0 CZ A:PHE244 4.0 50.2 1.0 CB A:ASP296 4.1 38.0 1.0 O4 A:OXL605 4.2 45.6 1.0 CE A:LYS270 4.3 31.2 1.0 OD1 A:ASP296 4.5 46.1 1.0 CG A:GLU272 4.5 39.0 1.0 O3 A:OXL605 4.5 38.8 1.0 OG A:SER243 4.6 37.3 1.0 CD2 A:PHE244 4.7 45.0 1.0 CE1 A:PHE244 4.9 45.2 1.0 CB A:GLU272 5.0 39.1 1.0 N A:ASP296 5.0 38.8 1.0

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


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-Asparagine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg609 b:50.5 occ:1.00 OE1 B:GLU272 2.1 44.9 1.0 OD2 B:ASP296 2.1 41.7 1.0 O1 B:OXL607 2.2 43.7 1.0 O2 B:OXL607 2.2 42.5 1.0 C2 B:OXL607 3.0 47.6 1.0 C1 B:OXL607 3.0 47.5 1.0 CD B:GLU272 3.2 47.7 1.0 CG B:ASP296 3.2 43.6 1.0 O1 B:GOL602 3.6 50.5 1.0 OE2 B:GLU272 3.6 50.8 1.0 CB B:ASP296 3.7 42.2 1.0 NZ B:LYS270 4.1 38.8 1.0 CZ B:PHE244 4.2 49.0 1.0 O4 B:OXL607 4.2 46.1 1.0 O3 B:OXL607 4.2 40.2 1.0 OD1 B:ASP296 4.3 37.0 1.0 N B:ASP296 4.3 42.2 1.0 CG B:GLU272 4.4 48.2 1.0 CE2 B:PHE244 4.6 53.1 1.0 CE B:LYS270 4.6 43.4 1.0 CA B:ASP296 4.7 37.8 1.0 CE1 B:PHE244 4.8 43.8 1.0 CB B:GLU272 4.8 50.3 1.0 CB B:ALA293 4.8 46.2 1.0 C1 B:GOL602 4.9 62.0 1.0 O2 B:GOL602 5.0 47.8 1.0

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


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-Asparagine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg604 b:57.5 occ:1.00 OD2 D:ASP296 2.3 52.5 1.0 O2 D:OXL602 2.4 59.5 1.0 O1 D:OXL602 2.7 62.8 1.0 C2 D:OXL602 3.2 56.9 1.0 C1 D:OXL602 3.4 61.0 1.0 OE1 D:GLU272 3.4 60.2 1.0 CG D:ASP296 3.4 57.8 1.0 OD1 D:ASP296 4.2 60.2 1.0 CB D:ASP296 4.3 52.7 1.0 O4 D:OXL602 4.3 54.5 1.0 CD D:GLU272 4.4 59.8 1.0 O3 D:OXL602 4.6 64.4 1.0 OE2 D:GLU272 4.6 58.5 1.0 NZ D:LYS270 4.6 55.6 1.0 O D:HOH709 4.7 48.6 1.0 N D:ASP296 4.8 56.8 1.0

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


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-Asparagine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg605 b:62.5 occ:1.00 CE1 D:TYR83 2.5 65.4 1.0 CG D:ARG56 3.0 62.8 1.0 CD1 D:TYR83 3.1 70.2 1.0 OE2 D:GLU86 3.5 62.6 1.0 CZ D:TYR83 3.5 63.7 1.0 OG1 D:THR87 3.8 59.7 1.0 OH D:TYR83 3.9 63.8 1.0 CB D:ARG56 4.0 56.7 1.0 CD D:GLU86 4.2 63.8 1.0 CG D:TYR83 4.3 66.8 1.0 O D:TYR83 4.3 60.2 1.0 CE2 D:TYR83 4.6 58.8 1.0 O D:HOH702 4.7 58.9 1.0 N D:THR87 4.8 51.6 1.0 CB D:GLU86 4.8 58.5 1.0 CG D:GLU86 4.8 58.2 1.0 CD2 D:TYR83 5.0 64.1 1.0 OE1 D:GLU86 5.0 66.5 1.0 CB D:THR87 5.0 53.9 1.0

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