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Magnesium in PDB 6wp4: Pyruvate Kinase M2 Mutant-S37E

Enzymatic activity of Pyruvate Kinase M2 Mutant-S37E

All present enzymatic activity of Pyruvate Kinase M2 Mutant-S37E:
2.7.1.40;

Protein crystallography data

The structure of Pyruvate Kinase M2 Mutant-S37E, PDB code: 6wp4 was solved by S.Nandi, M.Razzaghi, D.Srivastava, M.Dey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.53 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.167, 132.628, 110.128, 90.00, 112.74, 90.00
R / Rfree (%) 18.9 / 22.1

Other elements in 6wp4:

The structure of Pyruvate Kinase M2 Mutant-S37E also contains other interesting chemical elements:

Potassium (K) 5 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Mutant-S37E (pdb code 6wp4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyruvate Kinase M2 Mutant-S37E, PDB code: 6wp4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6wp4

Go back to Magnesium Binding Sites List in 6wp4
Magnesium binding site 1 out of 4 in the Pyruvate Kinase M2 Mutant-S37E


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-S37E within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:24.8
occ:1.00
O A:HOH787 2.0 22.4 1.0
O A:HOH779 2.0 25.6 1.0
O1 A:OXL606 2.1 31.0 1.0
OE1 A:GLU272 2.1 20.4 1.0
O2 A:OXL606 2.1 25.2 1.0
OD2 A:ASP296 2.2 27.8 1.0
C1 A:OXL606 2.8 29.9 1.0
C2 A:OXL606 2.8 26.1 1.0
CD A:GLU272 3.2 24.1 1.0
CG A:ASP296 3.3 27.1 1.0
OE2 A:GLU272 3.5 22.8 1.0
CB A:ASP296 3.8 17.8 1.0
NZ A:LYS270 4.0 21.8 1.0
O4 A:OXL606 4.1 26.8 1.0
O3 A:OXL606 4.1 32.4 1.0
N A:ASP296 4.3 17.7 1.0
CZ A:PHE244 4.3 26.7 1.0
O A:HOH861 4.4 41.6 1.0
OD1 A:ASP296 4.4 25.3 1.0
CE A:LYS270 4.5 20.9 1.0
O1 A:GOL612 4.5 40.1 1.0
O A:HOH783 4.5 20.6 1.0
CG A:GLU272 4.5 18.7 1.0
CA A:ASP296 4.7 19.9 1.0
CB A:ALA293 4.7 20.7 1.0
CB A:GLU272 4.7 22.0 1.0
CE2 A:PHE244 4.7 27.0 1.0
CE1 A:PHE244 4.8 27.3 1.0

Magnesium binding site 2 out of 4 in 6wp4

Go back to Magnesium Binding Sites List in 6wp4
Magnesium binding site 2 out of 4 in the Pyruvate Kinase M2 Mutant-S37E


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-S37E within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:27.7
occ:1.00
OD2 B:ASP296 2.1 24.4 1.0
OE1 B:GLU272 2.1 21.9 1.0
O B:HOH729 2.1 20.5 1.0
O B:HOH724 2.1 23.8 1.0
CD B:GLU272 3.1 26.6 1.0
CG B:ASP296 3.1 24.8 1.0
OE2 B:GLU272 3.5 24.5 1.0
CB B:ASP296 3.6 20.2 1.0
O B:HOH822 4.1 31.1 1.0
NZ B:LYS270 4.1 21.6 1.0
OD1 B:ASP296 4.2 25.9 1.0
N B:ASP296 4.3 23.0 1.0
CZ B:PHE244 4.3 27.1 1.0
CG B:GLU272 4.4 22.3 1.0
CE B:LYS270 4.5 22.0 1.0
CA B:ASP296 4.6 21.7 1.0
CB B:GLU272 4.6 23.9 1.0
O B:HOH764 4.6 23.2 1.0
CB B:ALA293 4.7 22.0 1.0
CE1 B:PHE244 4.8 30.8 1.0
CE2 B:PHE244 4.8 31.9 1.0

Magnesium binding site 3 out of 4 in 6wp4

Go back to Magnesium Binding Sites List in 6wp4
Magnesium binding site 3 out of 4 in the Pyruvate Kinase M2 Mutant-S37E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate Kinase M2 Mutant-S37E within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:35.6
occ:1.00
O C:HOH828 2.1 26.1 1.0
OE1 C:GLU272 2.1 25.3 1.0
CD C:GLU272 3.1 28.0 1.0
CG C:ASP296 3.3 28.4 1.0
OE2 C:GLU272 3.5 25.2 1.0
CB C:ASP296 3.7 24.8 1.0
O C:HOH819 3.9 30.4 1.0
NZ C:LYS270 3.9 22.2 1.0
CZ C:PHE244 4.3 27.0 1.0
N C:ASP296 4.3 25.6 1.0
CE C:LYS270 4.4 22.4 1.0
O1 C:GOL608 4.4 40.1 1.0
CG C:GLU272 4.5 24.2 1.0
O C:HOH743 4.6 24.8 1.0
CE2 C:PHE244 4.6 30.4 1.0
CB C:ALA293 4.7 23.7 1.0
CA C:ASP296 4.7 24.5 1.0
CB C:GLU272 4.7 27.5 1.0
C1 C:GOL608 4.8 40.4 1.0
CE1 C:PHE244 4.9 28.7 1.0

Magnesium binding site 4 out of 4 in 6wp4

Go back to Magnesium Binding Sites List in 6wp4
Magnesium binding site 4 out of 4 in the Pyruvate Kinase M2 Mutant-S37E


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate Kinase M2 Mutant-S37E within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:31.0
occ:1.00
O D:HOH757 2.0 27.2 1.0
O D:HOH722 2.0 28.3 1.0
OD2 D:ASP296 2.0 32.0 1.0
O4 D:OXL607 2.2 33.8 1.0
OE1 D:GLU272 2.2 28.6 1.0
O3 D:OXL607 2.2 25.4 1.0
C1 D:OXL607 2.9 26.6 1.0
C2 D:OXL607 2.9 33.4 1.0
CG D:ASP296 3.1 30.6 1.0
CD D:GLU272 3.2 28.4 1.0
OE2 D:GLU272 3.5 24.9 1.0
CB D:ASP296 3.6 21.7 1.0
CZ D:PHE244 4.1 29.3 1.0
O1 D:OXL607 4.1 25.6 1.0
NZ D:LYS270 4.1 24.6 1.0
O2 D:OXL607 4.1 36.5 1.0
OD1 D:ASP296 4.2 29.1 1.0
CE2 D:PHE244 4.4 32.4 1.0
N D:ASP296 4.4 24.4 1.0
O D:HOH719 4.5 26.3 1.0
CE D:LYS270 4.5 23.4 1.0
CG D:GLU272 4.5 26.1 1.0
CA D:ASP296 4.7 24.1 1.0
CB D:GLU272 4.8 25.8 1.0
CE1 D:PHE244 4.8 28.7 1.0
CB D:ALA293 4.8 26.1 1.0

Reference:

S.Nandi, M.Razzaghi, D.Srivastava, M.Dey. Structural Basis For Allosteric Regulation of Pyruvate Kinase M2 By Phosphorylation and Acetylation. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32989054
DOI: 10.1074/JBC.RA120.015800
Page generated: Tue Oct 1 23:06:09 2024

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