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Magnesium in PDB 5sc9: Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29, PDB code: 5sc9 was solved by A.Lulla, A.Foller, A.Nain-Perez, M.Grotli, P.Brear, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 187.85 / 1.69
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.273, 112.676, 187.899, 90, 91.34, 90
R / Rfree (%) 19.5 / 21.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29 (pdb code 5sc9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29, PDB code: 5sc9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5sc9

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Magnesium binding site 1 out of 10 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29


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 Anthraquinone Derivative 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:30.1
occ:1.00
 O2 A:OXL602 2.0 30.3 1.0
O A:HOH829 2.1 28.4 1.0
OE2 A:GLU284 2.1 30.2 1.0
O1 A:OXL602 2.1 28.3 1.0
OD2 A:ASP308 2.1 32.8 1.0
O A:HOH765 2.2 28.7 1.0
C1 A:OXL602 2.8 29.0 1.0
C2 A:OXL602 2.8 30.3 1.0
CD A:GLU284 3.2 30.9 1.0
CG A:ASP308 3.2 30.4 1.0
OE1 A:GLU284 3.5 31.2 1.0
CB A:ASP308 3.7 26.1 1.0
O A:HOH923 3.9 48.8 1.0
O4 A:OXL602 4.0 31.0 1.0
O3 A:OXL602 4.1 28.6 1.0
NZ A:LYS282 4.2 30.8 1.0
OD1 A:ASP308 4.3 31.1 1.0
N A:ASP308 4.4 24.3 1.0
CE A:LYS282 4.5 30.2 1.0
CG A:GLU284 4.5 28.4 1.0
O A:HOH794 4.6 45.1 1.0
CB A:ALA305 4.6 23.7 1.0
CA A:ASP308 4.7 24.5 1.0
CE2 A:PHE256 4.8 35.2 1.0
O A:HOH850 5.0 56.3 1.0
CB A:GLU284 5.0 24.3 1.0

Magnesium binding site 2 out of 10 in 5sc9

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Magnesium binding site 2 out of 10 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29


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 Anthraquinone Derivative 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:29.0
occ:1.00
 O4 B:OXL602 1.9 34.7 1.0
OE2 B:GLU284 2.0 32.7 1.0
OD2 B:ASP308 2.1 34.8 1.0
O B:HOH776 2.2 34.5 1.0
O B:HOH743 2.2 38.2 1.0
O3 B:OXL602 2.2 31.0 1.0
C2 B:OXL602 2.7 33.9 1.0
C1 B:OXL602 2.8 32.4 1.0
CD B:GLU284 3.1 33.0 1.0
CG B:ASP308 3.2 32.8 1.0
OE1 B:GLU284 3.5 35.0 1.0
CB B:ASP308 3.7 27.8 1.0
O2 B:OXL602 4.0 34.6 1.0
O1 B:OXL602 4.0 31.8 1.0
NZ B:LYS282 4.1 33.8 1.0
OD1 B:ASP308 4.3 34.4 1.0
CE B:LYS282 4.4 32.6 1.0
CG B:GLU284 4.4 29.3 1.0
N B:ASP308 4.4 24.8 1.0
CB B:ALA305 4.5 23.0 1.0
O B:HOH836 4.5 36.9 1.0
CA B:ASP308 4.7 25.2 1.0
CE1 B:PHE256 4.7 34.7 1.0
CB B:GLU284 4.9 26.7 1.0

Magnesium binding site 3 out of 10 in 5sc9

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Magnesium binding site 3 out of 10 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29


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 Anthraquinone Derivative 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:24.8
occ:1.00
 OD2 C:ASP308 2.0 27.3 1.0
OE2 C:GLU284 2.0 20.3 1.0
O C:HOH728 2.0 27.2 1.0
O3 C:OXL602 2.1 28.4 1.0
O4 C:OXL602 2.2 28.8 1.0
O C:HOH738 2.2 21.1 1.0
C1 C:OXL602 2.9 28.6 1.0
C2 C:OXL602 2.9 29.5 1.0
CD C:GLU284 3.1 21.1 1.0
CG C:ASP308 3.1 26.8 1.0
H12 C:I7K603 3.2 54.2 0.0
OE1 C:GLU284 3.5 21.0 1.0
CB C:ASP308 3.5 22.4 1.0
O C:HOH815 3.9 43.3 1.0
O5 C:I7K603 4.0 54.2 1.0
O1 C:OXL602 4.1 28.0 1.0
O2 C:OXL602 4.2 30.8 1.0
OD1 C:ASP308 4.2 28.6 1.0
NZ C:LYS282 4.2 21.9 1.0
N C:ASP308 4.3 19.8 1.0
CG C:GLU284 4.4 20.3 1.0
CE C:LYS282 4.5 21.0 1.0
CA C:ASP308 4.6 20.4 1.0
O C:HOH774 4.6 34.0 1.0
CB C:ALA305 4.6 18.0 1.0
CE1 C:PHE256 4.6 27.1 1.0
CB C:GLU284 4.8 19.5 1.0
CD1 C:PHE256 4.9 26.1 1.0

Magnesium binding site 4 out of 10 in 5sc9

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Magnesium binding site 4 out of 10 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29


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 Anthraquinone Derivative 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg605

b:20.2
occ:1.00
 OD1 C:ASN87 2.5 22.8 1.0
OD1 C:ASP125 2.6 25.6 1.0
O C:THR126 2.7 17.6 1.0
OG C:SER89 2.7 25.8 1.0
O C:HOH815 2.9 43.3 1.0
O C:HOH774 3.0 34.0 1.0
CG C:ASN87 3.6 22.3 1.0
C C:THR126 3.6 19.2 1.0
CG C:ASP125 3.6 23.7 1.0
OG C:SER255 3.7 19.0 1.0
O C:ASP125 3.7 17.2 1.0
CB C:SER89 3.7 24.4 1.0
O C:HOH925 3.9 44.8 1.0
N C:SER89 4.0 22.4 1.0
C C:ASP125 4.0 17.4 1.0
NZ C:LYS282 4.0 21.9 1.0
ND2 C:ASN87 4.1 22.3 1.0
CA C:LYS127 4.2 24.1 1.0
N C:LYS127 4.2 21.7 1.0
CB C:ASP125 4.3 18.4 1.0
NH2 C:ARG85 4.3 19.9 1.0
OD2 C:ASP125 4.4 25.1 1.0
N C:THR126 4.4 17.7 1.0
CA C:SER89 4.4 24.1 1.0
O C:LYS127 4.5 27.2 1.0
CA C:THR126 4.6 18.1 1.0
N C:PHE88 4.6 18.5 1.0
C C:LYS127 4.7 25.7 1.0
O C:HOH738 4.7 21.1 1.0
CB C:ASN87 4.7 19.0 1.0
CA C:ASP125 4.8 16.6 1.0
CA C:ASN87 4.8 17.3 1.0
CB C:SER255 4.9 16.8 1.0
C C:ASN87 4.9 18.1 1.0
C C:PHE88 5.0 21.6 1.0

Magnesium binding site 5 out of 10 in 5sc9

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Magnesium binding site 5 out of 10 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29


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 Anthraquinone Derivative 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:22.0
occ:1.00
 O D:HOH703 2.0 20.3 1.0
OD2 D:ASP308 2.0 24.7 1.0
OE2 D:GLU284 2.1 21.3 1.0
O D:HOH788 2.1 20.4 1.0
O1 D:OXL602 2.1 25.0 1.0
O2 D:OXL602 2.2 23.8 1.0
C1 D:OXL602 2.9 25.3 1.0
C2 D:OXL602 2.9 24.4 1.0
CD D:GLU284 3.1 21.2 1.0
CG D:ASP308 3.1 25.0 1.0
OE1 D:GLU284 3.5 21.6 1.0
H3 D:I7K603 3.6 31.7 0.0
CB D:ASP308 3.6 19.8 1.0
O4 D:I7K603 3.8 31.7 1.0
O D:HOH793 4.0 28.8 1.0
O4 D:OXL602 4.1 23.5 1.0
NZ D:LYS282 4.2 20.0 1.0
O3 D:OXL602 4.2 25.9 1.0
OD1 D:ASP308 4.2 26.1 1.0
N D:ASP308 4.4 18.5 1.0
CG D:GLU284 4.4 18.7 1.0
CE D:LYS282 4.5 19.8 1.0
O D:HOH804 4.5 22.0 1.0
CA D:ASP308 4.6 18.6 1.0
CE1 D:PHE256 4.6 28.3 1.0
CB D:ALA305 4.7 17.2 1.0
C8 D:I7K603 4.7 31.7 1.0
CB D:GLU284 4.9 18.3 1.0
C6 D:I7K603 4.9 31.6 1.0
CD1 D:PHE256 5.0 26.9 1.0

Magnesium binding site 6 out of 10 in 5sc9

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Magnesium binding site 6 out of 10 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29


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 Anthraquinone Derivative 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg604

b:28.8
occ:1.00
 OE2 E:GLU284 2.0 30.1 1.0
O3 E:OXL602 2.0 32.0 1.0
OD2 E:ASP308 2.1 34.7 1.0
O4 E:OXL602 2.1 29.3 1.0
O E:HOH824 2.2 32.0 1.0
O E:HOH753 2.2 28.7 1.0
C1 E:OXL602 2.7 32.5 1.0
C2 E:OXL602 2.8 31.0 1.0
CD E:GLU284 3.1 30.1 1.0
CG E:ASP308 3.2 31.4 1.0
OE1 E:GLU284 3.5 28.6 1.0
CB E:ASP308 3.6 26.2 1.0
O2 E:OXL602 4.0 31.0 1.0
O1 E:OXL602 4.1 33.6 1.0
NZ E:LYS282 4.2 32.5 1.0
OD1 E:ASP308 4.2 32.6 1.0
N E:ASP308 4.3 23.5 1.0
CG E:GLU284 4.4 28.8 1.0
CE E:LYS282 4.5 31.9 1.0
CB E:ALA305 4.5 23.4 1.0
CA E:ASP308 4.6 23.8 1.0
O E:HOH862 4.7 41.0 1.0
O E:HOH883 4.7 50.1 1.0
CE1 E:PHE256 4.8 34.6 1.0
CB E:GLU284 4.9 25.8 1.0

Magnesium binding site 7 out of 10 in 5sc9

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Magnesium binding site 7 out of 10 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29


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 Anthraquinone Derivative 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg604

b:24.3
occ:1.00
 OE2 F:GLU284 2.0 22.0 1.0
OD2 F:ASP308 2.0 27.4 1.0
O2 F:OXL602 2.1 27.1 1.0
O F:HOH791 2.1 23.3 1.0
O1 F:OXL602 2.1 25.5 1.0
O F:HOH785 2.2 21.7 1.0
C1 F:OXL602 2.9 26.1 1.0
C2 F:OXL602 2.9 27.8 1.0
CD F:GLU284 3.1 22.7 1.0
CG F:ASP308 3.1 25.9 1.0
OE1 F:GLU284 3.5 23.2 1.0
CB F:ASP308 3.6 20.7 1.0
O F:HOH919 4.0 36.9 1.0
O3 F:OXL602 4.1 24.9 1.0
O4 F:OXL602 4.1 29.3 1.0
O6 F:I7K603 4.1 51.8 1.0
NZ F:LYS282 4.2 22.1 1.0
OD1 F:ASP308 4.2 26.1 1.0
CG F:GLU284 4.4 22.2 1.0
N F:ASP308 4.4 18.1 1.0
CE F:LYS282 4.5 23.1 1.0
O F:HOH790 4.5 28.3 1.0
CB F:ALA305 4.5 17.2 1.0
CA F:ASP308 4.6 18.9 1.0
CE1 F:PHE256 4.7 29.5 1.0
CB F:GLU284 4.8 19.2 1.0
CD1 F:PHE256 5.0 28.0 1.0

Magnesium binding site 8 out of 10 in 5sc9

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Magnesium binding site 8 out of 10 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29


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 Anthraquinone Derivative 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg605

b:23.2
occ:1.00
 OD1 F:ASP125 2.6 31.8 1.0
O F:THR126 2.6 26.8 1.0
OD1 F:ASN87 2.7 27.1 1.0
OG F:SER89 2.7 33.4 1.0
O F:HOH790 2.9 28.3 1.0
O F:HOH919 2.9 36.9 1.0
C F:THR126 3.5 27.5 1.0
CG F:ASP125 3.6 29.9 1.0
OG F:SER255 3.6 25.7 1.0
CG F:ASN87 3.7 25.1 1.0
O F:ASP125 3.7 24.4 1.0
CB F:SER89 3.8 31.3 1.0
O F:HOH947 4.0 37.6 1.0
NZ F:LYS282 4.0 22.1 1.0
C F:ASP125 4.1 23.6 1.0
N F:SER89 4.1 29.2 1.0
CA F:LYS127 4.2 30.8 1.0
ND2 F:ASN87 4.2 25.2 1.0
N F:LYS127 4.2 28.6 1.0
CB F:ASP125 4.3 24.1 1.0
NH2 F:ARG85 4.4 24.1 1.0
OD2 F:ASP125 4.4 30.4 1.0
N F:THR126 4.4 24.1 1.0
O F:LYS127 4.5 32.4 1.0
CA F:SER89 4.5 30.9 1.0
O F:HOH785 4.6 21.7 1.0
CA F:THR126 4.6 25.8 1.0
C F:LYS127 4.6 32.0 1.0
N F:PHE88 4.7 24.1 1.0
CB F:SER255 4.8 23.9 1.0
CA F:ASP125 4.8 22.7 1.0
CB F:ASN87 4.8 22.2 1.0
CA F:ASN87 4.9 21.9 1.0

Magnesium binding site 9 out of 10 in 5sc9

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Magnesium binding site 9 out of 10 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg604

b:21.3
occ:1.00
 OE2 G:GLU284 2.0 19.1 1.0
O2 G:OXL602 2.0 24.9 1.0
O G:HOH743 2.1 20.3 1.0
O G:HOH707 2.1 20.8 1.0
OD2 G:ASP308 2.1 26.3 1.0
O1 G:OXL602 2.1 23.5 1.0
C2 G:OXL602 2.8 24.9 1.0
C1 G:OXL602 2.9 23.5 1.0
CD G:GLU284 3.0 20.6 1.0
CG G:ASP308 3.2 25.6 1.0
OE1 G:GLU284 3.4 18.8 1.0
CB G:ASP308 3.7 20.7 1.0
H3 G:I7K603 3.7 30.5 0.0
O4 G:I7K603 3.9 29.8 1.0
O G:HOH849 4.0 24.3 1.0
O3 G:OXL602 4.1 22.6 1.0
NZ G:LYS282 4.1 22.6 1.0
O4 G:OXL602 4.1 25.6 1.0
O G:HOH949 4.2 64.7 1.0
OD1 G:ASP308 4.3 28.7 1.0
CG G:GLU284 4.4 19.7 1.0
N G:ASP308 4.4 19.2 1.0
CE G:LYS282 4.4 21.0 1.0
O G:HOH1073 4.5 40.9 1.0
O G:HOH780 4.5 25.2 1.0
CB G:ALA305 4.6 17.2 1.0
CE1 G:PHE256 4.6 28.2 1.0
CA G:ASP308 4.7 19.2 1.0
C8 G:I7K603 4.8 30.5 1.0
CB G:GLU284 4.8 17.7 1.0
CD1 G:PHE256 4.9 27.0 1.0
C6 G:I7K603 5.0 29.9 1.0

Magnesium binding site 10 out of 10 in 5sc9

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Magnesium binding site 10 out of 10 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg604

b:20.1
occ:1.00
 OD2 H:ASP308 2.0 22.1 1.0
OE2 H:GLU284 2.0 18.6 1.0
O3 H:OXL602 2.1 20.1 1.0
O4 H:OXL602 2.1 18.8 1.0
O H:HOH801 2.1 19.6 1.0
O H:HOH723 2.1 18.8 1.0
C2 H:OXL602 2.8 19.1 1.0
C1 H:OXL602 2.9 20.9 1.0
CG H:ASP308 3.1 22.4 1.0
CD H:GLU284 3.1 18.4 1.0
OE1 H:GLU284 3.5 18.0 1.0
CB H:ASP308 3.6 17.3 1.0
H3 H:I7K603 3.8 25.1 0.0
O4 H:I7K603 3.9 23.4 1.0
O H:HOH895 3.9 29.1 1.0
O2 H:OXL602 4.1 18.0 1.0
O1 H:OXL602 4.1 23.0 1.0
OD1 H:ASP308 4.2 23.6 1.0
NZ H:LYS282 4.2 18.7 1.0
N H:ASP308 4.3 14.7 1.0
CG H:GLU284 4.4 16.0 1.0
CE H:LYS282 4.5 18.3 1.0
CA H:ASP308 4.6 14.8 1.0
CB H:ALA305 4.6 15.0 1.0
H1 H:I7K603 4.6 22.5 0.0
CE1 H:PHE256 4.6 26.2 1.0
O H:HOH737 4.7 23.2 1.0
CB H:GLU284 4.8 15.9 1.0
C8 H:I7K603 4.9 25.1 1.0
CD1 H:PHE256 5.0 25.3 1.0

Reference:

A.Nain-Perez, A.Foller Fuchtbauer, L.Haversen, A.Lulla, C.Gao, J.Matic, L.Monjas, A.Rodriguez, P.Brear, W.Kim, M.Hyvonen, J.Boren, A.Mardinoglu, M.Uhlen, M.Grotli. Anthraquinone Derivatives As Adp-Competitive Inhibitors of Liver Pyruvate Kinase. Eur.J.Med.Chem. V. 234 14270 2022.
ISSN: ISSN 0223-5234
PubMed: 35290845
DOI: 10.1016/J.EJMECH.2022.114270
Page generated: Tue Aug 12 19:06:28 2025

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