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Magnesium in PDB 5sci: Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105, PDB code: 5sci 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) 188.28 / 2.16
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 207.651, 112.839, 188.356, 90, 91.67, 90
R / Rfree (%) 20.6 / 22.9

Other elements in 5sci:

The structure of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105 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 105 (pdb code 5sci). 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 105, PDB code: 5sci:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5sci

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Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105


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

b:67.3
occ:1.00
 OD2 A:ASP308 2.0 74.8 1.0
O2 A:OXL602 2.3 68.5 1.0
O1 A:OXL602 2.3 68.7 1.0
OE2 A:GLU284 2.3 78.6 1.0
C1 A:OXL602 3.0 68.7 1.0
C2 A:OXL602 3.1 68.7 1.0
CG A:ASP308 3.2 73.1 1.0
CD A:GLU284 3.3 77.0 1.0
OE1 A:GLU284 3.6 80.1 1.0
CB A:ASP308 3.9 67.2 1.0
OD1 A:ASP308 4.2 74.3 1.0
NZ A:LYS282 4.2 65.0 1.0
O4 A:OXL602 4.3 68.6 1.0
O3 A:OXL602 4.3 69.0 1.0
N A:ASP308 4.6 63.0 1.0
CG A:GLU284 4.7 69.4 1.0
CE A:LYS282 4.7 64.5 1.0
CE1 A:PHE256 4.7 73.2 1.0
CA A:ASP308 4.9 64.3 1.0

Magnesium binding site 2 out of 8 in 5sci

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Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105


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

b:65.5
occ:1.00
 O4 B:OXL602 1.9 54.7 1.0
OE2 B:GLU284 2.0 66.2 1.0
OD2 B:ASP308 2.0 57.4 1.0
O B:HOH735 2.3 55.0 1.0
O3 B:OXL602 2.6 51.6 1.0
C2 B:OXL602 2.9 53.9 1.0
CD B:GLU284 2.9 64.2 1.0
CG B:ASP308 3.2 57.8 1.0
C1 B:OXL602 3.2 52.2 1.0
OE1 B:GLU284 3.2 66.1 1.0
CB B:ASP308 3.8 51.9 1.0
O2 B:OXL602 4.1 54.4 1.0
NZ B:LYS282 4.2 60.6 1.0
OD1 B:ASP308 4.2 60.3 1.0
CG B:GLU284 4.3 57.3 1.0
O1 B:OXL602 4.4 51.1 1.0
CE1 B:PHE256 4.5 61.2 1.0
CE B:LYS282 4.5 60.0 1.0
N B:ASP308 4.6 47.0 1.0
CB B:GLU284 4.7 53.6 1.0
CD1 B:PHE256 4.8 60.4 1.0
CB B:ALA305 4.8 45.5 1.0
CA B:ASP308 4.8 48.9 1.0

Magnesium binding site 3 out of 8 in 5sci

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Magnesium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105


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

b:55.9
occ:1.00
 OE2 C:GLU284 1.9 43.2 1.0
OD2 C:ASP308 2.2 54.1 1.0
O C:HOH704 2.3 48.0 1.0
O4 C:OXL602 2.3 63.2 1.0
O3 C:OXL602 2.5 61.6 1.0
CD C:GLU284 2.7 44.7 1.0
OE1 C:GLU284 2.9 46.0 1.0
C2 C:OXL602 3.2 62.6 1.0
C1 C:OXL602 3.3 61.8 1.0
CG C:ASP308 3.4 54.9 1.0
NZ C:LYS282 3.9 39.9 1.0
CB C:ASP308 4.0 50.2 1.0
CG C:GLU284 4.2 47.2 1.0
CE C:LYS282 4.3 40.5 1.0
CE1 C:PHE256 4.3 45.1 1.0
OD1 C:ASP308 4.4 57.5 1.0
O2 C:OXL602 4.4 62.5 1.0
H13 C:I9F605 4.5 95.8 0.0
CD1 C:PHE256 4.5 44.6 1.0
O1 C:OXL602 4.6 61.1 1.0
CB C:GLU284 4.7 46.0 1.0
OG C:SER255 4.8 43.1 1.0
CB C:ALA305 4.9 45.6 1.0
N C:ASP308 5.0 47.8 1.0
O4 C:I9F605 5.0 95.1 1.0

Magnesium binding site 4 out of 8 in 5sci

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Magnesium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105


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

b:54.8
occ:1.00
 OD2 D:ASP308 1.9 47.8 1.0
O2 D:OXL602 2.3 48.1 1.0
O1 D:OXL602 2.3 50.6 1.0
OE2 D:GLU284 2.5 49.7 1.0
C2 D:OXL602 3.0 48.8 1.0
C1 D:OXL602 3.0 49.7 1.0
CG D:ASP308 3.1 47.4 1.0
CD D:GLU284 3.6 46.6 1.0
CB D:ASP308 3.9 42.0 1.0
OE1 D:GLU284 3.9 47.7 1.0
OD1 D:ASP308 4.1 49.2 1.0
O4 D:OXL602 4.2 48.7 1.0
O3 D:OXL602 4.3 48.9 1.0
NZ D:LYS282 4.3 37.0 1.0
N D:ASP308 4.4 40.0 1.0
O D:HOH758 4.5 46.3 1.0
CA D:ASP308 4.8 40.7 1.0
CE D:LYS282 4.9 36.0 1.0
CG D:GLU284 4.9 44.0 1.0
CE1 D:PHE256 4.9 46.3 1.0

Magnesium binding site 5 out of 8 in 5sci

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Magnesium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105


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

b:62.4
occ:1.00
 OE2 E:GLU284 2.0 64.2 1.0
OD2 E:ASP308 2.1 66.9 1.0
O3 E:OXL602 2.1 68.7 1.0
O4 E:OXL602 2.4 68.1 1.0
C1 E:OXL602 2.9 68.7 1.0
CD E:GLU284 2.9 63.0 1.0
C2 E:OXL602 3.0 68.4 1.0
OE1 E:GLU284 3.2 63.2 1.0
CG E:ASP308 3.3 64.6 1.0
CB E:ASP308 3.9 59.0 1.0
NZ E:LYS282 4.0 55.6 1.0
O1 E:OXL602 4.2 68.6 1.0
O2 E:OXL602 4.2 68.4 1.0
CG E:GLU284 4.3 59.4 1.0
OD1 E:ASP308 4.3 65.6 1.0
CE E:LYS282 4.4 55.5 1.0
N E:ASP308 4.6 56.1 1.0
CE1 E:PHE256 4.6 66.8 1.0
CB E:ALA305 4.7 56.6 1.0
CB E:GLU284 4.7 56.9 1.0
O E:HOH752 4.8 76.7 1.0
CA E:ASP308 4.9 56.7 1.0
CD1 E:PHE256 4.9 66.1 1.0

Magnesium binding site 6 out of 8 in 5sci

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Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105


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

b:47.4
occ:1.00
 OD2 F:ASP308 2.0 49.0 1.0
O F:HOH801 2.2 42.1 1.0
O2 F:OXL602 2.2 60.6 1.0
OE2 F:GLU284 2.2 47.7 1.0
O1 F:OXL602 2.4 58.7 1.0
C2 F:OXL602 3.0 60.5 1.0
C1 F:OXL602 3.1 59.4 1.0
CD F:GLU284 3.2 48.6 1.0
CG F:ASP308 3.2 49.3 1.0
OE1 F:GLU284 3.5 51.9 1.0
CB F:ASP308 3.9 44.3 1.0
NZ F:LYS282 4.1 39.2 1.0
OD1 F:ASP308 4.2 52.1 1.0
O4 F:OXL602 4.2 61.0 1.0
O3 F:OXL602 4.3 59.2 1.0
N F:ASP308 4.5 40.6 1.0
CE F:LYS282 4.6 39.4 1.0
CG F:GLU284 4.6 45.4 1.0
CE1 F:PHE256 4.8 52.1 1.0
CA F:ASP308 4.8 42.4 1.0
CB F:ALA305 4.8 38.9 1.0
CB F:GLU284 5.0 43.9 1.0

Magnesium binding site 7 out of 8 in 5sci

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Magnesium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105


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

b:40.3
occ:1.00
 O G:HOH788 2.0 41.9 1.0
O1 G:OXL602 2.1 50.9 1.0
OE2 G:GLU284 2.1 43.0 1.0
OD2 G:ASP308 2.2 50.3 1.0
O2 G:OXL602 2.2 52.3 1.0
O G:HOH816 2.4 54.7 1.0
C1 G:OXL602 2.9 50.8 1.0
C2 G:OXL602 2.9 51.7 1.0
CD G:GLU284 3.1 43.7 1.0
OE1 G:GLU284 3.3 46.4 1.0
CG G:ASP308 3.3 50.2 1.0
O G:HOH878 3.8 71.8 1.0
NZ G:LYS282 4.0 42.1 1.0
CB G:ASP308 4.0 45.1 1.0
O3 G:OXL602 4.1 50.2 1.0
O4 G:OXL602 4.2 51.6 1.0
OD1 G:ASP308 4.4 52.1 1.0
CE G:LYS282 4.4 40.6 1.0
CG G:GLU284 4.5 40.8 1.0
O G:HOH837 4.6 64.7 1.0
N G:ASP308 4.7 44.5 1.0
CE1 G:PHE256 4.7 42.5 1.0
CB G:ALA305 4.8 41.0 1.0
CD1 G:PHE256 5.0 41.5 1.0
CB G:GLU284 5.0 39.1 1.0
CA G:ASP308 5.0 44.2 1.0

Magnesium binding site 8 out of 8 in 5sci

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Magnesium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 105


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

b:53.7
occ:1.00
 OD2 H:ASP308 1.9 43.6 1.0
O3 H:OXL602 2.1 44.6 1.0
OE2 H:GLU284 2.3 42.7 1.0
O4 H:OXL602 2.3 43.3 1.0
C1 H:OXL602 3.0 44.7 1.0
C2 H:OXL602 3.0 44.1 1.0
CG H:ASP308 3.1 41.8 1.0
CD H:GLU284 3.3 40.4 1.0
OE1 H:GLU284 3.5 41.5 1.0
CB H:ASP308 3.9 38.2 1.0
OD1 H:ASP308 4.1 43.0 1.0
O1 H:OXL602 4.1 45.3 1.0
NZ H:LYS282 4.2 34.1 1.0
O2 H:OXL602 4.2 44.5 1.0
N H:ASP308 4.5 37.0 1.0
CE1 H:PHE256 4.6 42.4 1.0
CE H:LYS282 4.6 35.0 1.0
CG H:GLU284 4.6 37.8 1.0
CA H:ASP308 4.8 37.8 1.0
CB H:ALA305 4.9 31.8 1.0
CD1 H:PHE256 4.9 41.7 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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