Magnesium in PDB 6wp5: Pyruvate Kinase M2 Mutant-S37D

Enzymatic activity of Pyruvate Kinase M2 Mutant-S37D

All present enzymatic activity of Pyruvate Kinase M2 Mutant-S37D:
2.7.1.40;

Protein crystallography data

The structure of Pyruvate Kinase M2 Mutant-S37D, PDB code: 6wp5 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) 19.84 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.625, 117.567, 109.965, 90.00, 112.63, 90.00
R / Rfree (%) 21.7 / 26

Other elements in 6wp5:

The structure of Pyruvate Kinase M2 Mutant-S37D also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate Kinase M2 Mutant-S37D (pdb code 6wp5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pyruvate Kinase M2 Mutant-S37D, PDB code: 6wp5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6wp5

Go back to Magnesium Binding Sites List in 6wp5
Magnesium binding site 1 out of 3 in the Pyruvate Kinase M2 Mutant-S37D


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-S37D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:33.5
occ:1.00
O B:HOH701 2.0 29.3 1.0
OD2 B:ASP296 2.0 27.8 1.0
O1 B:OXL606 2.1 29.4 1.0
O2 B:OXL606 2.1 35.5 1.0
O B:HOH716 2.1 32.0 1.0
OE1 B:GLU272 2.5 35.4 1.0
C1 B:OXL606 2.8 33.2 1.0
C2 B:OXL606 2.8 36.5 1.0
CG B:ASP296 3.0 31.3 1.0
CB B:ASP296 3.4 27.4 1.0
CD B:GLU272 3.7 36.0 1.0
O3 B:OXL606 4.0 30.8 1.0
O4 B:OXL606 4.0 38.2 1.0
N B:ASP296 4.1 25.6 1.0
OD1 B:ASP296 4.1 29.1 1.0
O B:HOH753 4.2 42.0 1.0
CZ B:PHE244 4.2 42.2 1.0
NZ B:LYS270 4.3 31.0 1.0
CA B:ASP296 4.4 29.2 1.0
CG B:GLU272 4.5 34.7 1.0
OE2 B:GLU272 4.5 36.8 1.0
CE2 B:PHE244 4.6 43.1 1.0
CE B:LYS270 4.6 29.3 1.0
CB B:GLU272 4.7 33.5 1.0
CB B:ALA293 4.7 26.6 1.0
CE1 B:PHE244 4.8 40.1 1.0

Magnesium binding site 2 out of 3 in 6wp5

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Magnesium binding site 2 out of 3 in the Pyruvate Kinase M2 Mutant-S37D


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-S37D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:36.4
occ:1.00
O A:HOH711 2.0 28.8 1.0
O3 A:OXL607 2.0 30.1 1.0
O4 A:OXL607 2.2 36.2 1.0
O A:HOH729 2.2 34.1 1.0
OE1 A:GLU272 2.2 34.5 1.0
OD2 A:ASP296 2.2 33.7 1.0
C1 A:OXL607 2.8 32.1 1.0
C2 A:OXL607 2.8 35.0 1.0
CG A:ASP296 3.3 35.4 1.0
CD A:GLU272 3.3 34.7 1.0
OE2 A:GLU272 3.6 33.1 1.0
CB A:ASP296 3.6 31.8 1.0
O1 A:OXL607 4.0 32.4 1.0
O2 A:OXL607 4.1 37.2 1.0
CZ A:PHE244 4.1 40.5 1.0
NZ A:LYS270 4.1 33.3 1.0
K A:K601 4.2 67.6 1.0
CE2 A:PHE244 4.3 43.1 1.0
N A:ASP296 4.3 29.1 1.0
OD1 A:ASP296 4.4 40.1 1.0
CE A:LYS270 4.5 32.0 1.0
CA A:ASP296 4.6 30.0 1.0
CG A:GLU272 4.6 33.2 1.0
CB A:GLU272 4.8 30.0 1.0
CB A:ALA293 4.8 29.0 1.0
CE1 A:PHE244 4.9 37.4 1.0

Magnesium binding site 3 out of 3 in 6wp5

Go back to Magnesium Binding Sites List in 6wp5
Magnesium binding site 3 out of 3 in the Pyruvate Kinase M2 Mutant-S37D


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-S37D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:49.7
occ:1.00
OD2 C:ASP296 2.0 44.0 1.0
O4 C:OXL605 2.1 46.4 1.0
O3 C:OXL605 2.4 46.2 1.0
OE1 C:GLU272 2.6 43.3 1.0
C2 C:OXL605 2.9 46.5 1.0
C1 C:OXL605 3.0 47.8 1.0
CG C:ASP296 3.2 45.8 1.0
CD C:GLU272 3.6 43.7 1.0
OE2 C:GLU272 3.8 47.3 1.0
CB C:ASP296 3.9 41.6 1.0
O2 C:OXL605 4.1 43.7 1.0
CZ C:PHE244 4.1 49.2 1.0
O C:HOH715 4.1 50.1 1.0
CE2 C:PHE244 4.2 53.8 1.0
OD1 C:ASP296 4.2 48.7 1.0
O1 C:OXL605 4.3 41.8 1.0
NZ C:LYS270 4.4 43.3 1.0
N C:ASP296 4.6 40.2 1.0
K C:K601 4.6 77.2 1.0
CE C:LYS270 4.7 37.1 1.0
CA C:ASP296 4.9 41.3 1.0
CG C:GLU272 4.9 42.9 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 Dec 15 01:36:49 2020

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