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Magnesium in PDB 5scl: Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1, PDB code: 5scl 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) 187.75 / 2.13
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 206.875, 112.269, 187.907, 90, 92.32, 90
R / Rfree (%) 19.8 / 22.2

Other elements in 5scl:

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

Magnesium binding site 1 out of 8 in 5scl

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Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:65.0
occ:1.00
 OD2 A:ASP308 2.1 60.9 1.0
OE2 A:GLU284 2.2 64.4 1.0
O2 A:OXL602 2.3 60.8 1.0
O1 A:OXL602 2.5 59.6 1.0
CD A:GLU284 3.1 61.6 1.0
C2 A:OXL602 3.2 60.6 1.0
C1 A:OXL602 3.3 59.5 1.0
CG A:ASP308 3.3 58.8 1.0
OE1 A:GLU284 3.4 61.0 1.0
CB A:ASP308 4.0 52.5 1.0
NZ A:LYS282 4.1 57.8 1.0
OD1 A:ASP308 4.3 60.2 1.0
O4 A:OXL602 4.4 61.1 1.0
O3 A:OXL602 4.5 58.7 1.0
CG A:GLU284 4.5 55.6 1.0
CE A:LYS282 4.5 56.3 1.0
CE1 A:PHE256 4.8 54.9 1.0
N A:ASP308 4.8 49.0 1.0
CD1 A:PHE256 4.9 54.0 1.0

Magnesium binding site 2 out of 8 in 5scl

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Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:50.4
occ:1.00
 O4 B:OXL602 1.9 54.9 1.0
OE2 B:GLU284 2.0 43.0 1.0
OD2 B:ASP308 2.1 55.5 1.0
O B:HOH773 2.3 45.5 1.0
O3 B:OXL602 2.5 52.1 1.0
C2 B:OXL602 2.9 54.2 1.0
CD B:GLU284 3.0 44.2 1.0
C1 B:OXL602 3.1 52.7 1.0
CG B:ASP308 3.2 53.6 1.0
OE1 B:GLU284 3.3 47.4 1.0
CB B:ASP308 3.8 48.1 1.0
O2 B:OXL602 4.1 54.6 1.0
NZ B:LYS282 4.1 45.7 1.0
O1 B:OXL602 4.3 51.7 1.0
OD1 B:ASP308 4.3 54.5 1.0
CG B:GLU284 4.3 44.0 1.0
CE B:LYS282 4.5 43.7 1.0
N B:ASP308 4.6 43.8 1.0
CE1 B:PHE256 4.7 47.6 1.0
CB B:ALA305 4.8 39.1 1.0
CB B:GLU284 4.8 43.5 1.0
CA B:ASP308 4.8 45.0 1.0
CD1 B:PHE256 4.9 46.8 1.0
O B:HOH865 4.9 59.3 1.0

Magnesium binding site 3 out of 8 in 5scl

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Magnesium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:57.6
occ:1.00
 OD2 C:ASP308 2.1 52.1 1.0
OE2 C:GLU284 2.2 44.7 1.0
O4 C:OXL602 2.3 61.6 1.0
O3 C:OXL602 2.3 60.9 1.0
C1 C:OXL602 3.1 60.8 1.0
C2 C:OXL602 3.1 61.5 1.0
CD C:GLU284 3.1 43.6 1.0
CG C:ASP308 3.2 51.0 1.0
OE1 C:GLU284 3.4 45.7 1.0
O C:HOH838 3.7 52.5 1.0
CB C:ASP308 3.8 44.6 1.0
NZ C:LYS282 4.1 42.6 1.0
OD1 C:ASP308 4.3 53.6 1.0
O2 C:OXL602 4.3 62.1 1.0
O1 C:OXL602 4.4 60.0 1.0
CG C:GLU284 4.5 42.3 1.0
CE C:LYS282 4.6 41.0 1.0
N C:ASP308 4.7 40.8 1.0
CE1 C:PHE256 4.8 41.4 1.0
CA C:ASP308 4.9 42.2 1.0
CB C:ALA305 4.9 37.0 1.0
CB C:GLU284 5.0 41.7 1.0
CD1 C:PHE256 5.0 40.9 1.0

Magnesium binding site 4 out of 8 in 5scl

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Magnesium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


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

b:49.0
occ:1.00
 OD2 D:ASP308 1.9 45.1 1.0
O D:HOH757 2.2 39.2 1.0
O1 D:OXL602 2.2 45.3 1.0
OE2 D:GLU284 2.3 45.3 1.0
O2 D:OXL602 2.3 42.4 1.0
C1 D:OXL602 3.0 44.0 1.0
C2 D:OXL602 3.1 43.2 1.0
CG D:ASP308 3.1 44.3 1.0
CD D:GLU284 3.3 41.4 1.0
OE1 D:GLU284 3.7 40.7 1.0
CB D:ASP308 3.8 38.9 1.0
OD1 D:ASP308 4.1 45.6 1.0
O4 D:OXL602 4.2 43.1 1.0
NZ D:LYS282 4.3 32.6 1.0
O3 D:OXL602 4.3 43.2 1.0
N D:ASP308 4.5 36.4 1.0
O D:HOH828 4.6 67.5 1.0
CG D:GLU284 4.7 36.6 1.0
CA D:ASP308 4.7 37.0 1.0
CE D:LYS282 4.8 30.3 1.0
CB D:ALA305 4.9 28.8 1.0
CE1 D:PHE256 4.9 39.5 1.0

Magnesium binding site 5 out of 8 in 5scl

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg604

b:56.6
occ:1.00
 OE2 E:GLU284 1.9 60.1 1.0
OD2 E:ASP308 2.2 60.1 1.0
O3 E:OXL602 2.3 64.5 1.0
O4 E:OXL602 2.3 62.8 1.0
O E:HOH755 2.4 54.1 1.0
CD E:GLU284 2.9 57.2 1.0
C1 E:OXL602 3.1 64.1 1.0
C2 E:OXL602 3.1 63.4 1.0
OE1 E:GLU284 3.2 57.0 1.0
CG E:ASP308 3.3 58.6 1.0
CB E:ASP308 3.8 50.9 1.0
NZ E:LYS282 3.9 49.4 1.0
CG E:GLU284 4.3 53.3 1.0
O2 E:OXL602 4.3 63.4 1.0
CE E:LYS282 4.3 49.0 1.0
O1 E:OXL602 4.4 63.8 1.0
OD1 E:ASP308 4.4 61.2 1.0
O E:HOH836 4.6 50.8 1.0
CB E:ALA305 4.6 47.3 1.0
N E:ASP308 4.6 47.4 1.0
CB E:GLU284 4.7 51.0 1.0
CE1 E:PHE256 4.8 54.3 1.0
CA E:ASP308 4.9 48.3 1.0
CD1 E:PHE256 4.9 53.7 1.0

Magnesium binding site 6 out of 8 in 5scl

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Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg604

b:45.9
occ:1.00
 OE2 F:GLU284 2.0 42.0 1.0
OD2 F:ASP308 2.0 49.9 1.0
O F:HOH728 2.1 37.9 1.0
O1 F:OXL602 2.2 61.9 1.0
O F:HOH750 2.3 56.4 1.0
O2 F:OXL602 2.3 63.3 1.0
CD F:GLU284 3.0 45.0 1.0
C1 F:OXL602 3.1 62.1 1.0
C2 F:OXL602 3.1 63.1 1.0
CG F:ASP308 3.1 49.5 1.0
OE1 F:GLU284 3.4 47.2 1.0
CB F:ASP308 3.6 43.9 1.0
NZ F:LYS282 4.2 47.6 1.0
OD1 F:ASP308 4.2 51.3 1.0
O3 F:OXL602 4.2 61.4 1.0
O4 F:OXL602 4.3 63.6 1.0
CG F:GLU284 4.3 42.4 1.0
O F:HOH814 4.4 52.0 1.0
N F:ASP308 4.5 39.3 1.0
CE F:LYS282 4.6 45.2 1.0
CA F:ASP308 4.7 40.9 1.0
CB F:ALA305 4.7 37.4 1.0
CE1 F:PHE256 4.7 46.1 1.0
CB F:GLU284 4.8 39.5 1.0
CD1 F:PHE256 4.9 45.4 1.0

Magnesium binding site 7 out of 8 in 5scl

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg604

b:39.3
occ:1.00
 O G:HOH766 1.9 31.9 1.0
OD2 G:ASP308 2.0 49.7 1.0
OE2 G:GLU284 2.2 44.9 1.0
O2 G:OXL602 2.2 45.7 1.0
O G:HOH714 2.3 42.3 1.0
O1 G:OXL602 2.3 45.2 1.0
C2 G:OXL602 3.0 45.2 1.0
C1 G:OXL602 3.1 45.2 1.0
CD G:GLU284 3.2 41.8 1.0
CG G:ASP308 3.2 46.8 1.0
OE1 G:GLU284 3.5 42.1 1.0
CB G:ASP308 3.8 42.5 1.0
O G:HOH924 4.0 64.6 1.0
O G:HOH780 4.1 41.8 1.0
NZ G:LYS282 4.2 38.1 1.0
OD1 G:ASP308 4.2 45.9 1.0
O3 G:OXL602 4.3 45.4 1.0
O4 G:OXL602 4.3 44.2 1.0
CG G:GLU284 4.5 39.4 1.0
O G:HOH825 4.6 57.6 1.0
N G:ASP308 4.6 39.7 1.0
CE G:LYS282 4.6 36.4 1.0
CE1 G:PHE256 4.8 39.8 1.0
CA G:ASP308 4.8 40.9 1.0
CB G:ALA305 4.9 36.8 1.0
CD1 G:PHE256 5.0 39.0 1.0
CB G:GLU284 5.0 37.5 1.0

Magnesium binding site 8 out of 8 in 5scl

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Magnesium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


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

b:45.0
occ:1.00
 OD2 H:ASP308 2.0 42.4 1.0
O4 H:OXL602 2.1 39.9 1.0
O3 H:OXL602 2.2 43.6 1.0
OE2 H:GLU284 2.2 42.7 1.0
O H:HOH743 2.3 39.1 1.0
C2 H:OXL602 2.9 41.2 1.0
C1 H:OXL602 2.9 42.9 1.0
CG H:ASP308 3.1 39.9 1.0
CD H:GLU284 3.3 40.1 1.0
CB H:ASP308 3.7 37.0 1.0
OE1 H:GLU284 3.7 38.8 1.0
O2 H:OXL602 4.1 41.4 1.0
O H:HOH885 4.1 49.7 1.0
OD1 H:ASP308 4.2 40.0 1.0
O1 H:OXL602 4.2 43.3 1.0
NZ H:LYS282 4.3 32.0 1.0
N H:ASP308 4.3 35.7 1.0
CA H:ASP308 4.6 36.3 1.0
CG H:GLU284 4.6 36.4 1.0
CE H:LYS282 4.7 29.9 1.0
CB H:ALA305 4.8 34.6 1.0
CB H:GLU284 5.0 35.0 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: Mon Sep 30 03:11:59 2024

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