Magnesium in PDB 4wj8: Human Pyruvate Kinase M2 Mutant C424A

All present enzymatic activity of Human Pyruvate Kinase M2 Mutant C424A:
2.7.1.40;

The structure of Human Pyruvate Kinase M2 Mutant C424A, PDB code: 4wj8 was solved by T.Mitchell, M.Yuan, I.Mcnae, H.Morgan, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.88 / 2.87
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	94.359, 115.260, 109.401, 90.00, 114.43, 90.00
R / Rfree (%)	20 / 24.3

The structure of Human Pyruvate Kinase M2 Mutant C424A also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Magnesium atom in the Human Pyruvate Kinase M2 Mutant C424A (pdb code 4wj8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Pyruvate Kinase M2 Mutant C424A, PDB code: 4wj8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Pyruvate Kinase M2 Mutant C424A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Pyruvate Kinase M2 Mutant C424A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:48.0 occ:1.00 OE2 A:GLU272 2.0 58.9 1.0 OD2 A:ASP296 2.1 62.4 1.0 O6 A:OXD601 2.1 49.1 1.0 O5 A:OXD601 2.5 55.0 1.0 C2 A:OXD601 3.0 50.8 1.0 C1 A:OXD601 3.1 53.1 1.0 CD A:GLU272 3.3 62.6 1.0 CG A:ASP296 3.3 61.0 1.0 NZ A:LYS270 3.7 51.9 1.0 CB A:ASP296 4.1 59.0 1.0 OE1 A:GLU272 4.1 61.0 1.0 O4 A:OXD601 4.1 50.3 1.0 CG A:GLU272 4.2 64.1 1.0 OD1 A:ASP296 4.2 60.5 1.0 O3 A:OXD601 4.4 51.8 1.0 N A:ASP296 4.6 56.7 1.0 CZ A:PHE244 4.6 68.7 1.0 CE2 A:PHE244 4.8 68.5 1.0 CA A:ASP296 5.0 57.6 1.0

Magnesium binding site 2 out of 4 in the Human Pyruvate Kinase M2 Mutant C424A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Pyruvate Kinase M2 Mutant C424A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:49.7 occ:1.00 OD2 B:ASP296 1.9 57.8 1.0 OE2 B:GLU272 2.0 49.3 1.0 O4 B:OXD601 2.3 51.2 1.0 O3 B:OXD601 2.5 54.5 1.0 CG B:ASP296 3.1 56.3 1.0 C2 B:OXD601 3.1 52.5 1.0 C1 B:OXD601 3.2 54.0 1.0 CD B:GLU272 3.2 51.3 1.0 NZ B:LYS270 3.8 59.2 1.0 CB B:ASP296 4.0 53.0 1.0 OD1 B:ASP296 4.0 57.7 1.0 OE1 B:GLU272 4.0 52.5 1.0 CG B:GLU272 4.2 52.3 1.0 CZ B:PHE244 4.3 64.3 1.0 O6 B:OXD601 4.3 50.5 1.0 O5 B:OXD601 4.5 54.4 1.0 CE2 B:PHE244 4.5 65.5 1.0 N B:ASP296 4.6 49.3 1.0 CA B:ASP296 4.9 51.1 1.0 O B:HOH715 5.0 39.4 1.0

Magnesium binding site 3 out of 4 in the Human Pyruvate Kinase M2 Mutant C424A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Pyruvate Kinase M2 Mutant C424A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:59.3 occ:1.00 OD2 C:ASP296 1.9 54.5 1.0 OE2 C:GLU272 2.2 67.3 1.0 O6 C:OXD602 2.3 66.0 1.0 O5 C:OXD602 2.3 68.0 1.0 C2 C:OXD602 3.0 67.6 1.0 C1 C:OXD602 3.1 68.3 1.0 CG C:ASP296 3.1 56.0 1.0 CD C:GLU272 3.4 71.0 1.0 CB C:ASP296 3.9 55.6 1.0 NZ C:LYS270 4.0 69.3 1.0 OD1 C:ASP296 4.0 54.8 1.0 O4 C:OXD602 4.2 63.8 1.0 OE1 C:GLU272 4.3 71.9 1.0 CG C:GLU272 4.3 72.0 1.0 O3 C:OXD602 4.3 69.7 1.0 N C:ASP296 4.3 55.4 1.0 CZ C:PHE244 4.6 76.1 1.0 CA C:ASP296 4.7 55.0 1.0 CE2 C:PHE244 4.9 75.6 1.0

Magnesium binding site 4 out of 4 in the Human Pyruvate Kinase M2 Mutant C424A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Pyruvate Kinase M2 Mutant C424A within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg604 b:46.5 occ:1.00 OD2 D:ASP296 2.0 49.0 1.0 OE2 D:GLU272 2.1 45.8 1.0 O3 D:OXD601 2.2 50.5 1.0 O4 D:OXD601 2.3 57.3 1.0 O D:HOH714 2.8 38.0 1.0 C1 D:OXD601 3.0 52.9 1.0 C2 D:OXD601 3.0 55.2 1.0 CG D:ASP296 3.2 46.8 1.0 CD D:GLU272 3.3 47.1 1.0 NZ D:LYS270 3.8 51.4 1.0 CB D:ASP296 4.1 45.6 1.0 OE1 D:GLU272 4.1 48.7 1.0 OD1 D:ASP296 4.1 46.4 1.0 O5 D:OXD601 4.2 52.2 1.0 O6 D:OXD601 4.2 54.2 1.0 CG D:GLU272 4.2 46.2 1.0 O D:HOH704 4.4 26.4 1.0 CZ D:PHE244 4.5 63.9 1.0 N D:ASP296 4.5 47.1 1.0 CE2 D:PHE244 4.8 62.8 1.0 CA D:ASP296 4.9 45.6 1.0

T.Mitchell, M.Yuan, I.Mcnae, H.Morgan, M.D.Walkinshaw. Human Pyruvate Kinase M2 Mutant C424A To Be Published.