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Magnesium in PDB 7frx: Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5, PDB code: 7frx 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) 189.12 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.844, 113.199, 189.15, 90, 90.99, 90
R / Rfree (%) 20 / 22.2

Other elements in 7frx:

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5 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 5 (pdb code 7frx). 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 5, PDB code: 7frx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7frx

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Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:36.1
occ:1.00
 OD2 A:ASP308 2.0 55.5 1.0
O2 A:OXL602 2.0 53.3 1.0
OE2 A:GLU284 2.1 59.6 1.0
O1 A:OXL602 2.1 52.5 1.0
O A:HOH807 2.4 45.8 1.0
O A:HOH753 2.6 43.7 1.0
C1 A:OXL602 2.8 52.9 1.0
C2 A:OXL602 2.8 53.4 1.0
CG A:ASP308 3.1 53.0 1.0
CD A:GLU284 3.1 58.7 1.0
OE1 A:GLU284 3.5 60.1 1.0
CB A:ASP308 3.6 47.9 1.0
O4 A:OXL602 4.0 53.8 1.0
O3 A:OXL602 4.0 52.7 1.0
OD1 A:ASP308 4.2 54.1 1.0
NZ A:LYS282 4.3 47.3 1.0
N A:ASP308 4.3 44.5 1.0
CG A:GLU284 4.4 52.4 1.0
CA A:ASP308 4.6 45.8 1.0
O A:HOH822 4.6 55.9 1.0
CE A:LYS282 4.6 47.9 1.0
CE1 A:PHE256 4.7 54.7 1.0
CB A:ALA305 4.8 38.0 1.0
CB A:GLU284 4.9 47.7 1.0

Magnesium binding site 2 out of 8 in 7frx

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Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:32.6
occ:1.00
 OE2 B:GLU284 1.9 40.7 1.0
O4 B:OXL602 2.0 47.7 1.0
OD2 B:ASP308 2.1 43.0 1.0
O B:HOH733 2.2 57.7 1.0
O3 B:OXL602 2.3 46.4 1.0
C2 B:OXL602 2.8 47.7 1.0
C1 B:OXL602 2.9 47.0 1.0
CD B:GLU284 3.0 44.0 1.0
CG B:ASP308 3.2 43.2 1.0
OE1 B:GLU284 3.4 47.8 1.0
CB B:ASP308 3.7 37.8 1.0
O2 B:OXL602 4.0 48.3 1.0
O1 B:OXL602 4.1 46.9 1.0
NZ B:LYS282 4.1 38.5 1.0
OD1 B:ASP308 4.3 45.9 1.0
CG B:GLU284 4.3 41.9 1.0
N B:ASP308 4.4 34.4 1.0
CE B:LYS282 4.4 38.5 1.0
O B:HOH780 4.5 54.3 1.0
CB B:ALA305 4.6 31.3 1.0
CA B:ASP308 4.7 35.3 1.0
CE1 B:PHE256 4.7 48.2 1.0
CB B:GLU284 4.8 39.1 1.0
CD1 B:PHE256 5.0 47.3 1.0

Magnesium binding site 3 out of 8 in 7frx

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Magnesium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:23.6
occ:1.00
 O C:HOH740 2.0 36.4 1.0
OE2 C:GLU284 2.0 33.8 1.0
O3 C:OXL602 2.0 40.1 1.0
OD2 C:ASP308 2.0 37.9 1.0
O4 C:OXL602 2.2 39.2 1.0
O C:HOH750 2.3 33.5 1.0
C1 C:OXL602 2.8 40.2 1.0
C2 C:OXL602 2.9 40.0 1.0
CD C:GLU284 3.1 34.4 1.0
CG C:ASP308 3.1 37.7 1.0
OE1 C:GLU284 3.5 33.5 1.0
CB C:ASP308 3.6 34.1 1.0
O C:HOH896 4.0 50.5 1.0
O1 C:OXL602 4.0 39.8 1.0
O2 C:OXL602 4.2 40.4 1.0
NZ C:LYS282 4.2 27.4 1.0
OD1 C:ASP308 4.2 39.4 1.0
O C:HOH1003 4.2 65.4 1.0
N C:ASP308 4.3 31.6 1.0
CG C:GLU284 4.4 34.0 1.0
O C:HOH921 4.5 35.5 1.0
CE C:LYS282 4.5 25.7 1.0
CA C:ASP308 4.6 32.5 1.0
CB C:ALA305 4.6 28.9 1.0
CE1 C:PHE256 4.7 38.3 1.0
CB C:GLU284 4.8 32.0 1.0

Magnesium binding site 4 out of 8 in 7frx

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Magnesium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:23.7
occ:1.00
 O1 D:OXL602 2.0 37.6 1.0
OD2 D:ASP308 2.1 36.3 1.0
OE2 D:GLU284 2.1 32.3 1.0
O D:HOH816 2.2 36.7 1.0
O2 D:OXL602 2.2 36.7 1.0
C1 D:OXL602 2.8 37.5 1.0
C2 D:OXL602 2.9 36.8 1.0
CD D:GLU284 3.1 30.8 1.0
CG D:ASP308 3.2 36.6 1.0
OE1 D:GLU284 3.5 30.8 1.0
CB D:ASP308 3.7 31.0 1.0
O D:HOH950 4.0 52.3 1.0
O3 D:OXL602 4.1 37.5 1.0
O4 D:OXL602 4.1 36.3 1.0
NZ D:LYS282 4.1 29.2 1.0
OD1 D:ASP308 4.2 38.8 1.0
N D:ASP308 4.3 29.3 1.0
CG D:GLU284 4.5 28.8 1.0
O D:HOH872 4.5 42.0 1.0
CE D:LYS282 4.5 28.0 1.0
CA D:ASP308 4.6 29.6 1.0
CB D:ALA305 4.7 24.9 1.0
CE1 D:PHE256 4.8 40.9 1.0
CB D:GLU284 4.9 29.4 1.0

Magnesium binding site 5 out of 8 in 7frx

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


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:33.1
occ:1.00
 OE2 E:GLU284 2.0 47.3 1.0
OD2 E:ASP308 2.0 47.2 1.0
O3 E:OXL602 2.0 52.5 1.0
O E:HOH790 2.2 43.7 1.0
O4 E:OXL602 2.3 51.6 1.0
C1 E:OXL602 2.8 52.6 1.0
C2 E:OXL602 2.9 52.1 1.0
CD E:GLU284 3.0 46.8 1.0
CG E:ASP308 3.1 45.1 1.0
OE1 E:GLU284 3.5 47.5 1.0
CB E:ASP308 3.6 40.4 1.0
O1 E:OXL602 4.0 52.8 1.0
O2 E:OXL602 4.1 52.0 1.0
O E:HOH887 4.1 58.6 1.0
OD1 E:ASP308 4.2 46.4 1.0
NZ E:LYS282 4.2 45.6 1.0
O E:HOH844 4.2 67.9 1.0
N E:ASP308 4.3 38.4 1.0
CG E:GLU284 4.3 43.4 1.0
CE E:LYS282 4.6 45.0 1.0
CA E:ASP308 4.6 39.0 1.0
CE1 E:PHE256 4.6 51.9 1.0
CB E:ALA305 4.7 36.8 1.0
CB E:GLU284 4.8 41.0 1.0
CD1 E:PHE256 4.9 51.2 1.0

Magnesium binding site 6 out of 8 in 7frx

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Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg603

b:26.0
occ:1.00
 OE2 F:GLU284 1.9 37.5 1.0
O F:HOH731 2.0 33.8 1.0
OD2 F:ASP308 2.1 40.8 1.0
O1 F:OXL602 2.2 41.3 1.0
O2 F:OXL602 2.2 42.3 1.0
O F:HOH744 2.3 38.6 1.0
C1 F:OXL602 2.9 41.3 1.0
CD F:GLU284 3.0 37.4 1.0
C2 F:OXL602 3.0 42.5 1.0
CG F:ASP308 3.1 39.6 1.0
OE1 F:GLU284 3.4 39.0 1.0
CB F:ASP308 3.6 32.5 1.0
O3 F:OXL602 4.1 40.4 1.0
NZ F:LYS282 4.2 33.2 1.0
O4 F:OXL602 4.2 43.3 1.0
O F:HOH939 4.2 58.9 1.0
OD1 F:ASP308 4.2 42.7 1.0
CG F:GLU284 4.3 35.8 1.0
N F:ASP308 4.4 29.3 1.0
CE F:LYS282 4.5 34.5 1.0
CB F:ALA305 4.6 27.8 1.0
CA F:ASP308 4.6 30.3 1.0
CE1 F:PHE256 4.7 41.3 1.0
CB F:GLU284 4.8 32.4 1.0
CD1 F:PHE256 4.9 40.0 1.0

Magnesium binding site 7 out of 8 in 7frx

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Magnesium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:19.5
occ:1.00
 OE2 G:GLU284 2.0 33.8 1.0
O2 G:OXL602 2.1 35.2 1.0
OD2 G:ASP308 2.1 36.2 1.0
O G:HOH827 2.1 37.1 1.0
O G:HOH748 2.2 38.2 1.0
O1 G:OXL602 2.2 36.0 1.0
C2 G:OXL602 2.8 35.4 1.0
C1 G:OXL602 2.9 35.3 1.0
CD G:GLU284 3.0 31.9 1.0
CG G:ASP308 3.2 37.1 1.0
OE1 G:GLU284 3.4 27.1 1.0
CB G:ASP308 3.7 32.0 1.0
O G:HOH920 4.0 41.1 1.0
O3 G:OXL602 4.1 34.8 1.0
O4 G:OXL602 4.1 35.8 1.0
NZ G:LYS282 4.2 28.0 1.0
OD1 G:ASP308 4.3 41.0 1.0
CG G:GLU284 4.4 31.7 1.0
N G:ASP308 4.4 30.2 1.0
CE G:LYS282 4.5 26.2 1.0
O G:HOH859 4.5 39.0 1.0
CA G:ASP308 4.7 30.1 1.0
CE1 G:PHE256 4.7 35.9 1.0
CB G:ALA305 4.7 27.6 1.0
CB G:GLU284 4.8 29.0 1.0
O G:HOH1036 4.9 61.2 1.0
CD1 G:PHE256 4.9 35.1 1.0

Magnesium binding site 8 out of 8 in 7frx

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


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:20.0
occ:1.00
 OE2 H:GLU284 2.0 29.6 1.0
OD2 H:ASP308 2.0 35.0 1.0
O3 H:OXL602 2.1 34.2 1.0
O4 H:OXL602 2.2 33.1 1.0
O H:HOH828 2.2 39.1 1.0
O H:HOH777 2.3 30.3 1.0
C2 H:OXL602 2.8 33.1 1.0
C1 H:OXL602 2.9 34.3 1.0
CD H:GLU284 3.1 30.3 1.0
CG H:ASP308 3.1 34.5 1.0
OE1 H:GLU284 3.5 30.4 1.0
CB H:ASP308 3.6 29.0 1.0
O2 H:OXL602 4.1 31.9 1.0
O1 H:OXL602 4.1 35.0 1.0
NZ H:LYS282 4.2 24.4 1.0
OD1 H:ASP308 4.2 37.0 1.0
N H:ASP308 4.3 25.8 1.0
O H:HOH1019 4.3 62.0 1.0
CG H:GLU284 4.4 28.3 1.0
O H:HOH963 4.4 43.9 1.0
CE H:LYS282 4.5 24.7 1.0
CA H:ASP308 4.5 26.8 1.0
CB H:ALA305 4.6 21.6 1.0
CE1 H:PHE256 4.7 36.2 1.0
CB H:GLU284 4.8 26.8 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 21:36:53 2024

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