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Magnesium in PDB 7fs0: Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8, PDB code: 7fs0 was solved by A.Lulla, O.Nilsson, P.Brear, A.Nain-Perez, M.Grotli, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 189.45 / 2.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.002, 113.344, 189.484, 90, 91.12, 90
R / Rfree (%) 21.9 / 25.3

Other elements in 7fs0:

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 also contains other interesting chemical elements:

Potassium (K) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 (pdb code 7fs0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8, PDB code: 7fs0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7fs0

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Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:62.0
occ:1.00
 O1 A:OXL602 2.0 144.1 1.0
OD2 A:ASP308 2.0 92.1 1.0
OE2 A:GLU284 2.1 96.2 1.0
O2 A:OXL602 2.1 144.2 1.0
C1 A:OXL602 2.7 144.1 1.0
C2 A:OXL602 2.8 144.1 1.0
CD A:GLU284 3.2 93.8 1.0
CG A:ASP308 3.2 90.4 1.0
OE1 A:GLU284 3.6 95.4 1.0
CB A:ASP308 3.9 86.3 1.0
O3 A:OXL602 3.9 144.1 1.0
O4 A:OXL602 4.0 144.0 1.0
OD1 A:ASP308 4.2 91.2 1.0
NZ A:LYS282 4.3 87.2 1.0
CG A:GLU284 4.5 87.0 1.0
N A:ASP308 4.5 84.2 1.0
CE A:LYS282 4.7 84.7 1.0
CB A:ALA305 4.8 80.4 1.0
CA A:ASP308 4.8 84.9 1.0
CE1 A:PHE256 4.9 95.9 1.0
CB A:GLU284 5.0 81.9 1.0
O A:HOH740 5.0 63.8 1.0

Magnesium binding site 2 out of 8 in 7fs0

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Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:59.8
occ:1.00
 O4 B:OXL602 2.0 80.0 1.0
OD2 B:ASP308 2.0 70.0 1.0
OE2 B:GLU284 2.1 84.7 1.0
O3 B:OXL602 2.1 77.3 1.0
C2 B:OXL602 2.7 79.3 1.0
C1 B:OXL602 2.8 78.0 1.0
CG B:ASP308 3.2 69.6 1.0
CD B:GLU284 3.2 84.0 1.0
OE1 B:GLU284 3.6 87.6 1.0
CB B:ASP308 3.8 63.3 1.0
O1 B:OXL602 4.0 77.7 1.0
O2 B:OXL602 4.0 79.2 1.0
OD1 B:ASP308 4.2 72.1 1.0
NZ B:LYS282 4.3 82.7 1.0
N B:ASP308 4.4 58.2 1.0
CG B:GLU284 4.5 76.2 1.0
CE B:LYS282 4.7 80.3 1.0
CA B:ASP308 4.8 59.8 1.0
CB B:ALA305 4.8 55.5 1.0
CE1 B:PHE256 4.9 83.8 1.0
CB B:GLU284 5.0 71.0 1.0

Magnesium binding site 3 out of 8 in 7fs0

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Magnesium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:56.5
occ:1.00
 OE2 C:GLU284 1.9 54.2 1.0
OD2 C:ASP308 2.0 79.6 1.0
O3 C:OXL602 2.1 78.2 1.0
O4 C:OXL602 2.1 78.9 1.0
O C:HOH719 2.4 55.9 1.0
C1 C:OXL602 2.9 78.2 1.0
CD C:GLU284 2.9 58.5 1.0
C2 C:OXL602 2.9 78.5 1.0
CG C:ASP308 3.2 77.7 1.0
OE1 C:GLU284 3.3 63.1 1.0
CB C:ASP308 3.9 71.5 1.0
O2 C:OXL602 4.1 78.3 1.0
O1 C:OXL602 4.2 78.0 1.0
NZ C:LYS282 4.2 61.0 1.0
OD1 C:ASP308 4.2 79.2 1.0
CG C:GLU284 4.3 56.5 1.0
CE C:LYS282 4.6 58.1 1.0
CE1 C:PHE256 4.7 57.2 1.0
N C:ASP308 4.7 67.9 1.0
CB C:GLU284 4.8 55.1 1.0
CB C:ALA305 4.9 60.8 1.0
CD1 C:PHE256 4.9 56.4 1.0
CA C:ASP308 4.9 69.3 1.0

Magnesium binding site 4 out of 8 in 7fs0

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Magnesium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:36.5
occ:1.00
 OD2 D:ASP308 1.9 58.3 1.0
O2 D:OXL602 2.0 62.6 1.0
OE2 D:GLU284 2.2 58.1 1.0
O1 D:OXL602 2.5 64.8 1.0
C2 D:OXL602 2.9 63.0 1.0
CG D:ASP308 3.1 56.6 1.0
C1 D:OXL602 3.2 63.9 1.0
CD D:GLU284 3.3 57.2 1.0
OE1 D:GLU284 3.7 58.1 1.0
CB D:ASP308 3.9 51.9 1.0
OD1 D:ASP308 4.1 57.4 1.0
O4 D:OXL602 4.1 62.4 1.0
NZ D:LYS282 4.3 44.9 1.0
O3 D:OXL602 4.4 63.6 1.0
N D:ASP308 4.6 48.9 1.0
CG D:GLU284 4.6 54.2 1.0
CE D:LYS282 4.8 41.6 1.0
CA D:ASP308 4.8 49.9 1.0
CE1 D:PHE256 4.9 54.4 1.0
CB D:ALA305 5.0 41.2 1.0

Magnesium binding site 5 out of 8 in 7fs0

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Magnesium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:46.8
occ:1.00
 OE2 E:GLU284 1.9 75.2 1.0
OD2 E:ASP308 1.9 83.3 1.0
O4 E:OXL602 2.0 89.2 1.0
O3 E:OXL602 2.2 89.8 1.0
C2 E:OXL602 2.7 89.4 1.0
C1 E:OXL602 2.8 89.9 1.0
CD E:GLU284 3.0 75.5 1.0
CG E:ASP308 3.1 79.9 1.0
OE1 E:GLU284 3.5 76.8 1.0
CB E:ASP308 3.7 73.2 1.0
O2 E:OXL602 3.9 89.4 1.0
O1 E:OXL602 4.1 90.0 1.0
OD1 E:ASP308 4.1 80.8 1.0
NZ E:LYS282 4.3 71.7 1.0
CG E:GLU284 4.3 72.2 1.0
N E:ASP308 4.4 69.6 1.0
CA E:ASP308 4.7 70.4 1.0
CE E:LYS282 4.7 70.9 1.0
CB E:ALA305 4.7 65.3 1.0
CB E:GLU284 4.8 69.5 1.0
CE1 E:PHE256 4.8 78.3 1.0

Magnesium binding site 6 out of 8 in 7fs0

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Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg603

b:38.4
occ:1.00
 OD2 F:ASP308 2.0 58.5 1.0
O1 F:OXL602 2.2 90.0 1.0
OE2 F:GLU284 2.2 52.1 1.0
O2 F:OXL602 2.3 91.2 1.0
C1 F:OXL602 3.0 90.3 1.0
C2 F:OXL602 3.1 90.8 1.0
CG F:ASP308 3.2 57.0 1.0
CD F:GLU284 3.3 54.0 1.0
OE1 F:GLU284 3.6 57.7 1.0
CB F:ASP308 3.9 49.8 1.0
OD1 F:ASP308 4.1 60.1 1.0
O3 F:OXL602 4.2 90.1 1.0
NZ F:LYS282 4.3 51.7 1.0
O4 F:OXL602 4.3 90.8 1.0
CG F:GLU284 4.6 48.9 1.0
N F:ASP308 4.6 44.9 1.0
CE F:LYS282 4.7 49.3 1.0
CA F:ASP308 4.9 47.1 1.0
CE1 F:PHE256 4.9 59.6 1.0
CB F:ALA305 4.9 41.9 1.0

Magnesium binding site 7 out of 8 in 7fs0

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Magnesium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:31.3
occ:1.00
 O1 G:OXL602 1.9 56.0 1.0
OE2 G:GLU284 2.0 49.1 1.0
OD2 G:ASP308 2.1 64.1 1.0
O2 G:OXL602 2.4 58.2 1.0
C1 G:OXL602 2.8 56.4 1.0
C2 G:OXL602 3.0 57.6 1.0
CD G:GLU284 3.0 50.8 1.0
OE1 G:GLU284 3.3 53.7 1.0
CG G:ASP308 3.3 61.8 1.0
O G:HOH759 3.8 63.7 1.0
O3 G:OXL602 4.0 55.7 1.0
NZ G:LYS282 4.0 40.5 1.0
CB G:ASP308 4.0 55.3 1.0
O4 G:OXL602 4.3 58.0 1.0
OD1 G:ASP308 4.3 63.2 1.0
CG G:GLU284 4.4 47.3 1.0
CE G:LYS282 4.5 39.9 1.0
CE1 G:PHE256 4.8 48.8 1.0
N G:ASP308 4.8 51.5 1.0
CB G:ALA305 4.9 48.5 1.0
CB G:GLU284 5.0 44.1 1.0
CD1 G:PHE256 5.0 48.0 1.0

Magnesium binding site 8 out of 8 in 7fs0

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Magnesium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:28.8
occ:1.00
 O4 H:OXL602 1.9 54.3 1.0
OE2 H:GLU284 1.9 54.9 1.0
OD2 H:ASP308 2.0 54.8 1.0
O3 H:OXL602 2.6 56.5 1.0
O H:HOH851 2.8 47.2 1.0
C2 H:OXL602 2.9 55.4 1.0
CD H:GLU284 3.0 52.5 1.0
CG H:ASP308 3.2 52.1 1.0
C1 H:OXL602 3.2 56.2 1.0
OE1 H:GLU284 3.3 56.1 1.0
CB H:ASP308 3.9 46.1 1.0
O2 H:OXL602 4.1 55.8 1.0
NZ H:LYS282 4.1 42.1 1.0
OD1 H:ASP308 4.2 52.9 1.0
CG H:GLU284 4.3 45.3 1.0
O1 H:OXL602 4.4 56.5 1.0
CE H:LYS282 4.5 39.8 1.0
O H:HOH928 4.7 46.9 1.0
CE1 H:PHE256 4.7 47.2 1.0
O H:HOH901 4.7 55.5 1.0
N H:ASP308 4.7 42.3 1.0
CB H:GLU284 4.8 42.0 1.0
CB H:ALA305 4.9 33.8 1.0
CD1 H:PHE256 4.9 46.4 1.0
CA H:ASP308 4.9 43.9 1.0

Reference:

A.Nain-Perez, O.Nilsson, A.Lulla, L.Haversen, P.Brear, S.Liljenberg, M.Hyvonen, J.Boren, M.Grotli. Tuning Liver Pyruvate Kinase Activity Up or Down with A New Class of Allosteric Modulators. Eur.J.Med.Chem. V. 250 15177 2023.
ISSN: ISSN 0223-5234
PubMed: 36753880
DOI: 10.1016/J.EJMECH.2023.115177
Page generated: Wed Oct 2 21:38:01 2024

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