Magnesium in PDB 5x0i: Crystal Structure of PKM2 R399E Mutant Complexed with Fbp and Serine

Enzymatic activity of Crystal Structure of PKM2 R399E Mutant Complexed with Fbp and Serine

All present enzymatic activity of Crystal Structure of PKM2 R399E Mutant Complexed with Fbp and Serine:
2.7.1.40;

Protein crystallography data

The structure of Crystal Structure of PKM2 R399E Mutant Complexed with Fbp and Serine, PDB code: 5x0i was solved by W.C.Wang, T.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.601, 137.875, 149.709, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.8

Other elements in 5x0i:

The structure of Crystal Structure of PKM2 R399E Mutant Complexed with Fbp and Serine also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PKM2 R399E Mutant Complexed with Fbp and Serine (pdb code 5x0i). 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 PKM2 R399E Mutant Complexed with Fbp and Serine, PDB code: 5x0i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5x0i

Go back to Magnesium Binding Sites List in 5x0i
Magnesium binding site 1 out of 4 in the Crystal Structure of PKM2 R399E Mutant Complexed with Fbp and Serine


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 PKM2 R399E Mutant Complexed with Fbp and Serine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:28.1
occ:1.00
 OE1 A:GLU272 2.1 29.3 1.0
O2 A:PYR603 2.2 41.2 1.0
O3 A:PYR603 2.2 38.9 1.0
OD2 A:ASP296 2.2 39.5 1.0
C2 A:PYR603 2.9 36.3 1.0
C1 A:PYR603 3.0 38.7 1.0
CD A:GLU272 3.1 32.7 1.0
OE2 A:GLU272 3.3 37.3 1.0
CG A:ASP296 3.4 40.9 1.0
CB A:ASP296 3.9 34.1 1.0
NZ A:LYS270 4.1 26.3 1.0
O1 A:PYR603 4.2 38.5 1.0
CZ A:PHE244 4.3 33.1 1.0
C3 A:PYR603 4.4 37.9 1.0
OD1 A:ASP296 4.4 43.2 1.0
CG A:GLU272 4.5 29.4 1.0
N A:ASP296 4.6 25.3 1.0
CE A:LYS270 4.6 25.9 1.0
CE2 A:PHE244 4.7 32.3 1.0
CB A:ALA293 4.8 26.8 1.0
CB A:GLU272 4.9 33.3 1.0
CE1 A:PHE244 4.9 32.5 1.0
CA A:ASP296 4.9 28.5 1.0

Magnesium binding site 2 out of 4 in 5x0i

Go back to Magnesium Binding Sites List in 5x0i
Magnesium binding site 2 out of 4 in the Crystal Structure of PKM2 R399E Mutant Complexed with Fbp and Serine


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 PKM2 R399E Mutant Complexed with Fbp and Serine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:33.7
occ:1.00
 OD2 B:ASP296 2.1 36.0 1.0
O3 B:PYR603 2.1 25.2 1.0
O2 B:PYR603 2.4 30.6 1.0
OE1 B:GLU272 2.4 41.9 1.0
C2 B:PYR603 3.0 25.8 1.0
C1 B:PYR603 3.1 32.0 1.0
CG B:ASP296 3.3 37.5 1.0
CD B:GLU272 3.3 41.0 1.0
OE2 B:GLU272 3.5 45.0 1.0
O B:HOH703 3.9 31.9 1.0
NZ B:LYS270 3.9 35.1 1.0
CZ B:PHE244 4.1 44.8 1.0
CB B:ASP296 4.2 37.6 1.0
OD1 B:ASP296 4.2 37.6 1.0
O1 B:PYR603 4.4 35.0 1.0
C3 B:PYR603 4.4 24.0 1.0
CE2 B:PHE244 4.5 43.7 1.0
CE B:LYS270 4.5 33.7 1.0
CG B:GLU272 4.7 35.5 1.0
CE1 B:PHE244 4.8 43.2 1.0
N B:ASP296 4.9 34.4 1.0

Magnesium binding site 3 out of 4 in 5x0i

Go back to Magnesium Binding Sites List in 5x0i
Magnesium binding site 3 out of 4 in the Crystal Structure of PKM2 R399E Mutant Complexed with Fbp and Serine


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 PKM2 R399E Mutant Complexed with Fbp and Serine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:35.8
occ:1.00
 O3 C:PYR603 1.7 34.8 1.0
OD2 C:ASP296 1.9 38.7 1.0
OE1 C:GLU272 2.2 41.8 1.0
O1 C:PYR603 2.8 35.0 1.0
C2 C:PYR603 2.8 34.5 1.0
CD C:GLU272 3.1 46.4 1.0
CG C:ASP296 3.1 37.1 1.0
C1 C:PYR603 3.2 36.6 1.0
OE2 C:GLU272 3.3 55.7 1.0
NZ C:LYS270 3.9 35.7 1.0
CB C:ASP296 3.9 30.3 1.0
OD1 C:ASP296 4.1 33.6 1.0
C3 C:PYR603 4.1 30.9 1.0
CZ C:PHE244 4.2 39.6 1.0
CE C:LYS270 4.3 35.8 1.0
CE2 C:PHE244 4.3 43.6 1.0
O2 C:PYR603 4.5 38.5 1.0
CG C:GLU272 4.5 39.1 1.0
CB C:GLU272 4.9 37.9 1.0
N C:ASP296 4.9 29.2 1.0
CE1 C:PHE244 4.9 39.3 1.0

Magnesium binding site 4 out of 4 in 5x0i

Go back to Magnesium Binding Sites List in 5x0i
Magnesium binding site 4 out of 4 in the Crystal Structure of PKM2 R399E Mutant Complexed with Fbp and Serine


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 PKM2 R399E Mutant Complexed with Fbp and Serine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:46.1
occ:1.00
 O3 D:PYR603 2.0 45.7 1.0
OD2 D:ASP296 2.1 42.3 1.0
OE1 D:GLU272 2.4 39.7 1.0
C2 D:PYR603 3.0 41.6 1.0
O1 D:PYR603 3.1 46.9 1.0
CD D:GLU272 3.2 38.2 1.0
OE2 D:GLU272 3.3 39.1 1.0
CG D:ASP296 3.3 45.2 1.0
C1 D:PYR603 3.5 45.9 1.0
CZ D:PHE244 3.6 44.7 1.0
CE2 D:PHE244 3.7 46.5 1.0
NZ D:LYS270 3.9 38.2 1.0
C3 D:PYR603 4.2 40.9 1.0
OD1 D:ASP296 4.2 43.9 1.0
CB D:ASP296 4.3 40.1 1.0
CE D:LYS270 4.3 37.0 1.0
CE1 D:PHE244 4.4 48.8 1.0
CD2 D:PHE244 4.6 43.9 1.0
OG D:SER243 4.6 31.0 1.0
CG D:GLU272 4.6 36.7 1.0
O2 D:PYR603 4.8 41.7 1.0
CB D:SER243 4.8 33.6 1.0
K D:K605 4.9 52.7 1.0

Reference:

T.J.Chen, H.J.Wang, J.S.Liu, H.H.Cheng, S.C.Hsu, M.C.Wu, C.H.Lu, Y.F.Wu, J.W.Wu, Y.Y.Liu, H.J.Kung, W.C.Wang. Mutations in the PKM2 Exon-10 Region Are Associated with Reduced Allostery and Increased Nuclear Translocation. Commun Biol V. 2 105 2019.
ISSN: ESSN 2399-3642
PubMed: 30911680
DOI: 10.1038/S42003-019-0343-4
Page generated: Mon Dec 14 21:26:02 2020

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