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

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 7

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 7:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 7, PDB code: 7frz 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) 187.67 / 2.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 207.176, 112.984, 187.82, 90, 92.26, 90
R / Rfree (%) 21.2 / 24.1

Other elements in 7frz:

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

Magnesium binding site 1 out of 8 in 7frz

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Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 7


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

b:52.9
occ:1.00
 OD2 A:ASP308 2.0 74.4 1.0
O2 A:OXL602 2.2 81.7 1.0
OE2 A:GLU284 2.2 79.7 1.0
O1 A:OXL602 2.3 81.2 1.0
C2 A:OXL602 2.9 81.6 1.0
C1 A:OXL602 3.0 81.2 1.0
CD A:GLU284 3.2 77.5 1.0
CG A:ASP308 3.2 72.2 1.0
OE1 A:GLU284 3.4 78.3 1.0
CB A:ASP308 3.9 66.1 1.0
NZ A:LYS282 4.1 69.3 1.0
O4 A:OXL602 4.1 81.6 1.0
OD1 A:ASP308 4.1 73.3 1.0
O3 A:OXL602 4.2 81.1 1.0
CG A:GLU284 4.6 71.3 1.0
CE A:LYS282 4.6 67.8 1.0
N A:ASP308 4.7 62.7 1.0
CE1 A:PHE256 4.7 76.3 1.0
CA A:ASP308 4.9 63.9 1.0
CB A:ALA305 5.0 58.7 1.0
CD1 A:PHE256 5.0 75.5 1.0

Magnesium binding site 2 out of 8 in 7frz

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Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 7


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

b:45.0
occ:1.00
 O4 B:OXL602 1.9 65.2 1.0
OD2 B:ASP308 1.9 58.0 1.0
OE2 B:GLU284 2.0 65.7 1.0
O3 B:OXL602 2.4 63.7 1.0
C2 B:OXL602 2.8 64.9 1.0
C1 B:OXL602 3.0 64.0 1.0
CD B:GLU284 3.0 62.8 1.0
CG B:ASP308 3.1 55.0 1.0
OE1 B:GLU284 3.4 64.2 1.0
CB B:ASP308 3.7 47.9 1.0
O2 B:OXL602 4.0 65.1 1.0
OD1 B:ASP308 4.1 55.6 1.0
NZ B:LYS282 4.2 61.9 1.0
O1 B:OXL602 4.2 63.3 1.0
CG B:GLU284 4.3 55.1 1.0
N B:ASP308 4.5 42.9 1.0
O B:HOH799 4.5 58.9 1.0
CE B:LYS282 4.6 59.1 1.0
CB B:ALA305 4.7 39.5 1.0
CE1 B:PHE256 4.7 58.3 1.0
CA B:ASP308 4.7 44.8 1.0
CB B:GLU284 4.8 50.1 1.0
CD1 B:PHE256 4.9 57.6 1.0

Magnesium binding site 3 out of 8 in 7frz

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Magnesium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 7


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

b:38.9
occ:1.00
 OE2 C:GLU284 2.0 52.6 1.0
OD2 C:ASP308 2.0 66.0 1.0
O3 C:OXL602 2.1 69.9 1.0
O4 C:OXL602 2.6 70.7 1.0
CD C:GLU284 2.9 51.4 1.0
C1 C:OXL602 2.9 70.1 1.0
C2 C:OXL602 3.1 70.5 1.0
OE1 C:GLU284 3.2 54.1 1.0
CG C:ASP308 3.2 63.6 1.0
CB C:ASP308 3.9 56.9 1.0
NZ C:LYS282 4.0 48.8 1.0
O1 C:OXL602 4.1 69.8 1.0
OD1 C:ASP308 4.2 65.4 1.0
CG C:GLU284 4.3 49.9 1.0
O2 C:OXL602 4.3 70.4 1.0
CE C:LYS282 4.4 46.5 1.0
CE1 C:PHE256 4.6 50.6 1.0
N C:ASP308 4.7 53.1 1.0
CB C:GLU284 4.8 50.2 1.0
CB C:ALA305 4.8 49.5 1.0
CD1 C:PHE256 4.8 49.4 1.0
CA C:ASP308 4.9 54.3 1.0

Magnesium binding site 4 out of 8 in 7frz

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Magnesium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 7


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

b:28.1
occ:1.00
 OD2 D:ASP308 1.9 50.1 1.0
OE2 D:GLU284 2.1 47.5 1.0
O2 D:OXL602 2.1 56.0 1.0
O1 D:OXL602 2.3 56.5 1.0
C2 D:OXL602 2.9 56.1 1.0
C1 D:OXL602 3.0 56.0 1.0
CG D:ASP308 3.1 48.1 1.0
CD D:GLU284 3.1 46.4 1.0
OE1 D:GLU284 3.5 49.4 1.0
CB D:ASP308 3.8 43.3 1.0
O4 D:OXL602 4.1 55.9 1.0
OD1 D:ASP308 4.1 48.6 1.0
NZ D:LYS282 4.2 37.3 1.0
O3 D:OXL602 4.3 55.2 1.0
CG D:GLU284 4.5 43.1 1.0
N D:ASP308 4.5 40.3 1.0
CE D:LYS282 4.6 31.5 1.0
O D:HOH739 4.6 47.4 1.0
O D:HOH909 4.7 51.2 1.0
CB D:ALA305 4.7 31.3 1.0
CA D:ASP308 4.8 41.4 1.0
CE1 D:PHE256 4.8 45.6 1.0
CB D:GLU284 4.9 40.7 1.0

Magnesium binding site 5 out of 8 in 7frz

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


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

b:49.2
occ:1.00
 OD2 E:ASP308 1.9 67.4 1.0
O3 E:OXL602 2.0 75.8 1.0
OE2 E:GLU284 2.0 71.0 1.0
O4 E:OXL602 2.3 75.0 1.0
C1 E:OXL602 2.8 75.6 1.0
C2 E:OXL602 3.0 75.1 1.0
CD E:GLU284 3.0 69.3 1.0
CG E:ASP308 3.1 63.8 1.0
OE1 E:GLU284 3.3 69.6 1.0
CB E:ASP308 3.8 56.8 1.0
O1 E:OXL602 4.1 75.7 1.0
NZ E:LYS282 4.1 56.8 1.0
OD1 E:ASP308 4.1 64.7 1.0
O2 E:OXL602 4.2 74.7 1.0
CG E:GLU284 4.4 64.9 1.0
CE E:LYS282 4.5 56.7 1.0
N E:ASP308 4.6 52.6 1.0
CE1 E:PHE256 4.7 66.5 1.0
CB E:ALA305 4.8 51.0 1.0
CA E:ASP308 4.8 53.7 1.0
CB E:GLU284 4.8 60.0 1.0
CD1 E:PHE256 4.9 65.5 1.0

Magnesium binding site 6 out of 8 in 7frz

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Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 7


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

b:32.6
occ:1.00
 O2 F:OXL602 1.9 70.0 1.0
OD2 F:ASP308 2.0 54.2 1.0
OE2 F:GLU284 2.1 50.0 1.0
O1 F:OXL602 2.1 69.7 1.0
C2 F:OXL602 2.8 69.8 1.0
C1 F:OXL602 2.8 69.3 1.0
CG F:ASP308 3.1 53.0 1.0
CD F:GLU284 3.2 51.0 1.0
O F:HOH824 3.6 66.3 1.0
OE1 F:GLU284 3.6 55.0 1.0
CB F:ASP308 3.8 44.6 1.0
O4 F:OXL602 4.0 69.8 1.0
O3 F:OXL602 4.0 68.7 1.0
OD1 F:ASP308 4.1 55.9 1.0
NZ F:LYS282 4.2 41.6 1.0
N F:ASP308 4.4 39.7 1.0
CG F:GLU284 4.5 44.2 1.0
CE F:LYS282 4.6 39.1 1.0
CB F:ALA305 4.7 36.2 1.0
CA F:ASP308 4.7 40.6 1.0
CE1 F:PHE256 4.9 51.9 1.0
CB F:GLU284 4.9 41.7 1.0

Magnesium binding site 7 out of 8 in 7frz

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


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

b:23.5
occ:1.00
 OE2 G:GLU284 2.0 44.1 1.0
OD2 G:ASP308 2.0 57.3 1.0
O2 G:OXL602 2.2 54.2 1.0
O G:HOH745 2.2 43.4 1.0
O1 G:OXL602 2.3 52.2 1.0
CD G:GLU284 2.9 44.9 1.0
C2 G:OXL602 2.9 53.7 1.0
C1 G:OXL602 3.0 52.5 1.0
OE1 G:GLU284 3.2 46.9 1.0
CG G:ASP308 3.2 54.4 1.0
CB G:ASP308 3.9 48.7 1.0
NZ G:LYS282 4.0 37.2 1.0
O3 G:OXL602 4.2 51.8 1.0
OD1 G:ASP308 4.2 54.9 1.0
O4 G:OXL602 4.2 53.9 1.0
CG G:GLU284 4.3 43.2 1.0
CE G:LYS282 4.4 35.1 1.0
CE1 G:PHE256 4.7 42.9 1.0
N G:ASP308 4.7 45.1 1.0
CB G:ALA305 4.7 39.5 1.0
CB G:GLU284 4.8 41.2 1.0
CD1 G:PHE256 4.8 41.9 1.0
CA G:ASP308 4.9 46.0 1.0

Magnesium binding site 8 out of 8 in 7frz

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


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

b:22.1
occ:1.00
 OD2 H:ASP308 1.9 44.0 1.0
OE2 H:GLU284 2.0 36.8 1.0
O4 H:OXL602 2.1 49.6 1.0
O3 H:OXL602 2.1 50.4 1.0
O H:HOH710 2.1 32.0 1.0
O H:HOH765 2.2 41.6 1.0
C2 H:OXL602 2.8 50.0 1.0
C1 H:OXL602 2.8 50.8 1.0
CD H:GLU284 3.1 35.6 1.0
CG H:ASP308 3.1 41.9 1.0
OE1 H:GLU284 3.4 36.8 1.0
CB H:ASP308 3.7 36.7 1.0
O2 H:OXL602 4.1 49.6 1.0
O1 H:OXL602 4.1 51.4 1.0
O H:HOH855 4.1 52.8 1.0
OD1 H:ASP308 4.1 43.6 1.0
NZ H:LYS282 4.1 26.7 1.0
O H:HOH871 4.2 49.8 1.0
CG H:GLU284 4.4 33.2 1.0
N H:ASP308 4.4 34.2 1.0
CE H:LYS282 4.5 24.8 1.0
CB H:ALA305 4.6 26.6 1.0
CA H:ASP308 4.7 35.7 1.0
CE1 H:PHE256 4.8 40.6 1.0
CB H:GLU284 4.8 32.1 1.0
O H:HOH894 5.0 49.0 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 21:37:30 2024

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