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Potassium 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:

Magnesium (Mg) 8 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 8 binding sites of Potassium where determined in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1, PDB code: 5scl:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 5scl

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Potassium 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 Potassium with other atoms in the K 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:K605

b:78.7
occ:1.00
 OD1 A:ASN87 2.5 61.0 1.0
OG A:SER89 2.7 68.6 1.0
OD1 A:ASP125 2.8 67.9 1.0
O A:THR126 2.8 69.5 1.0
CG A:ASN87 3.7 60.5 1.0
CG A:ASP125 3.7 67.4 1.0
C A:THR126 3.7 69.0 1.0
OG A:SER255 3.7 54.9 1.0
CB A:SER89 3.8 66.5 1.0
O A:ASP125 4.0 61.5 1.0
NZ A:LYS282 4.0 57.8 1.0
CA A:LYS127 4.2 73.6 1.0
ND2 A:ASN87 4.2 61.5 1.0
N A:SER89 4.2 64.9 1.0
C A:ASP125 4.3 61.9 1.0
N A:LYS127 4.3 71.1 1.0
NH2 A:ARG85 4.3 53.5 1.0
CB A:ASP125 4.4 61.6 1.0
OD2 A:ASP125 4.4 70.2 1.0
O A:LYS127 4.5 75.5 1.0
CA A:SER89 4.6 65.5 1.0
N A:THR126 4.6 63.7 1.0
C A:LYS127 4.6 75.3 1.0
CA A:THR126 4.8 66.0 1.0
N A:PHE88 4.8 61.9 1.0
CB A:ASN87 4.9 58.3 1.0
CB A:SER255 4.9 52.9 1.0
CA A:ASN87 5.0 58.0 1.0
CA A:ASP125 5.0 59.8 1.0
O2 A:OXL602 5.0 60.8 1.0

Potassium binding site 2 out of 8 in 5scl

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Potassium 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 Potassium with other atoms in the K 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:K605

b:64.7
occ:1.00
 O B:THR126 2.7 56.5 1.0
OD1 B:ASN87 2.7 46.5 1.0
OD1 B:ASP125 2.7 60.6 1.0
OG B:SER89 2.7 53.4 1.0
OG B:SER255 3.5 43.7 1.0
C B:THR126 3.7 56.0 1.0
CG B:ASP125 3.7 59.6 1.0
CG B:ASN87 3.8 47.9 1.0
CB B:SER89 3.8 52.2 1.0
NZ B:LYS282 3.9 45.7 1.0
O B:ASP125 4.1 48.7 1.0
CA B:LYS127 4.2 60.9 1.0
N B:LYS127 4.3 58.1 1.0
N B:SER89 4.3 51.6 1.0
ND2 B:ASN87 4.3 48.8 1.0
C B:ASP125 4.3 49.2 1.0
O B:LYS127 4.4 63.1 1.0
NH2 B:ARG85 4.4 42.5 1.0
CB B:ASP125 4.4 52.0 1.0
OD2 B:ASP125 4.5 62.6 1.0
C B:LYS127 4.6 63.0 1.0
CA B:SER89 4.6 52.1 1.0
N B:THR126 4.6 50.5 1.0
CB B:SER255 4.7 43.2 1.0
CA B:THR126 4.8 52.8 1.0
N B:PHE88 5.0 50.5 1.0

Potassium binding site 3 out of 8 in 5scl

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Potassium 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 Potassium with other atoms in the K 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:K605

b:56.4
occ:1.00
 OD1 C:ASN87 2.4 43.4 1.0
OG C:SER89 2.8 45.3 1.0
OD1 C:ASP125 2.8 50.9 1.0
O C:HOH838 2.9 52.5 1.0
O C:THR126 3.0 43.5 1.0
CG C:ASN87 3.5 42.3 1.0
CG C:ASP125 3.6 49.4 1.0
CB C:SER89 3.8 43.4 1.0
OG C:SER255 3.9 38.8 1.0
C C:THR126 3.9 44.3 1.0
NZ C:LYS282 3.9 42.6 1.0
ND2 C:ASN87 4.0 42.0 1.0
O C:ASP125 4.1 42.5 1.0
NH2 C:ARG85 4.1 40.1 1.0
N C:SER89 4.2 42.0 1.0
CB C:ASP125 4.3 43.2 1.0
OD2 C:ASP125 4.3 52.2 1.0
C C:ASP125 4.4 42.6 1.0
CA C:LYS127 4.4 47.3 1.0
N C:LYS127 4.5 45.9 1.0
CA C:SER89 4.6 42.9 1.0
O C:LYS127 4.7 48.6 1.0
CB C:ASN87 4.7 41.4 1.0
N C:THR126 4.8 42.6 1.0
N C:PHE88 4.8 41.4 1.0
C C:LYS127 4.9 47.3 1.0
CA C:ASN87 4.9 41.2 1.0
O4 C:OXL602 4.9 61.6 1.0
CA C:THR126 5.0 43.1 1.0
CA C:ASP125 5.0 41.4 1.0

Potassium binding site 4 out of 8 in 5scl

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Potassium 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 Potassium with other atoms in the K 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:K604

b:49.6
occ:1.00
 OD1 D:ASN87 2.6 31.9 1.0
OG D:SER89 2.6 40.6 1.0
O D:THR126 2.7 39.5 1.0
OD1 D:ASP125 2.7 37.7 1.0
CG D:ASP125 3.6 38.1 1.0
C D:THR126 3.6 39.6 1.0
OG D:SER255 3.6 37.6 1.0
CG D:ASN87 3.7 32.6 1.0
CB D:SER89 3.7 38.3 1.0
O D:ASP125 3.9 37.0 1.0
NZ D:LYS282 4.0 32.6 1.0
N D:SER89 4.1 36.3 1.0
C D:ASP125 4.1 35.7 1.0
CA D:LYS127 4.2 43.8 1.0
N D:LYS127 4.2 41.4 1.0
ND2 D:ASN87 4.3 32.7 1.0
CB D:ASP125 4.3 34.7 1.0
O D:LYS127 4.3 48.0 1.0
O D:HOH757 4.4 39.2 1.0
NH2 D:ARG85 4.4 40.5 1.0
OD2 D:ASP125 4.4 40.1 1.0
CA D:SER89 4.5 37.3 1.0
N D:THR126 4.5 35.9 1.0
C D:LYS127 4.6 46.7 1.0
CA D:THR126 4.6 36.9 1.0
N D:PHE88 4.7 34.2 1.0
CB D:SER255 4.8 35.6 1.0
CA D:ASP125 4.8 34.3 1.0
CB D:ASN87 4.8 32.6 1.0
CA D:ASN87 4.9 32.9 1.0

Potassium binding site 5 out of 8 in 5scl

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Potassium 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 Potassium with other atoms in the K 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:K605

b:79.0
occ:1.00
 OD1 E:ASN87 2.4 54.9 1.0
O E:THR126 2.6 61.4 1.0
OG E:SER89 2.7 64.7 1.0
OD1 E:ASP125 2.7 59.4 1.0
C E:THR126 3.5 60.9 1.0
CG E:ASN87 3.6 53.2 1.0
CG E:ASP125 3.6 58.8 1.0
O E:ASP125 3.7 55.0 1.0
CB E:SER89 3.7 62.1 1.0
OG E:SER255 3.8 50.2 1.0
N E:SER89 3.9 59.7 1.0
C E:ASP125 4.0 55.2 1.0
CA E:LYS127 4.0 64.4 1.0
N E:LYS127 4.1 62.6 1.0
NZ E:LYS282 4.2 49.4 1.0
CB E:ASP125 4.2 55.2 1.0
ND2 E:ASN87 4.2 52.3 1.0
CA E:SER89 4.4 60.7 1.0
N E:THR126 4.4 56.3 1.0
NH2 E:ARG85 4.4 41.9 1.0
N E:PHE88 4.5 55.9 1.0
OD2 E:ASP125 4.5 59.9 1.0
CA E:THR126 4.5 58.3 1.0
O E:LYS127 4.6 66.2 1.0
C E:LYS127 4.6 66.0 1.0
CB E:ASN87 4.7 52.4 1.0
CA E:ASP125 4.7 54.1 1.0
CA E:ASN87 4.8 52.9 1.0
C E:PHE88 4.8 59.1 1.0
C E:ASN87 4.8 54.9 1.0
CB E:SER255 5.0 49.9 1.0

Potassium binding site 6 out of 8 in 5scl

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Potassium 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 Potassium with other atoms in the K 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:K605

b:59.6
occ:1.00
 OD1 F:ASN87 2.4 41.6 1.0
O F:HOH814 2.6 52.0 1.0
OD1 F:ASP125 2.6 56.2 1.0
O F:THR126 2.7 52.1 1.0
OG F:SER89 2.8 53.8 1.0
CG F:ASP125 3.5 54.6 1.0
CG F:ASN87 3.5 42.1 1.0
C F:THR126 3.6 52.7 1.0
O F:ASP125 3.7 46.6 1.0
OG F:SER255 3.8 43.7 1.0
CB F:SER89 3.8 50.4 1.0
C F:ASP125 4.0 47.2 1.0
N F:SER89 4.1 49.5 1.0
NZ F:LYS282 4.1 47.6 1.0
CB F:ASP125 4.1 48.0 1.0
ND2 F:ASN87 4.1 42.6 1.0
CA F:LYS127 4.2 58.1 1.0
N F:LYS127 4.2 55.0 1.0
NH2 F:ARG85 4.3 40.8 1.0
OD2 F:ASP125 4.3 57.4 1.0
N F:THR126 4.4 48.3 1.0
N F:PHE88 4.5 47.8 1.0
CA F:SER89 4.5 49.8 1.0
CA F:THR126 4.6 50.4 1.0
CB F:ASN87 4.7 42.1 1.0
O F:LYS127 4.7 60.4 1.0
CA F:ASP125 4.7 46.2 1.0
CA F:ASN87 4.7 43.1 1.0
C F:LYS127 4.7 60.1 1.0
C F:ASN87 4.8 46.1 1.0
O F:HOH750 4.8 56.4 1.0
C F:PHE88 4.9 49.7 1.0

Potassium binding site 7 out of 8 in 5scl

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Potassium 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 Potassium with other atoms in the K 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:K605

b:54.9
occ:1.00
 OD1 G:ASN87 2.5 37.9 1.0
OG G:SER89 2.7 42.5 1.0
OD1 G:ASP125 2.7 44.3 1.0
O G:THR126 2.7 39.5 1.0
O G:HOH780 2.9 41.8 1.0
CG G:ASN87 3.6 38.1 1.0
CG G:ASP125 3.6 43.6 1.0
C G:THR126 3.6 39.3 1.0
CB G:SER89 3.8 40.4 1.0
OG G:SER255 3.8 36.5 1.0
O G:ASP125 3.9 34.7 1.0
NZ G:LYS282 4.1 38.1 1.0
N G:SER89 4.1 39.0 1.0
CA G:LYS127 4.1 42.0 1.0
C G:ASP125 4.2 35.2 1.0
ND2 G:ASN87 4.2 39.5 1.0
N G:LYS127 4.2 40.6 1.0
CB G:ASP125 4.2 36.4 1.0
NH2 G:ARG85 4.3 36.4 1.0
O G:HOH807 4.4 49.1 1.0
OD2 G:ASP125 4.4 47.1 1.0
CA G:SER89 4.5 39.5 1.0
N G:THR126 4.5 35.7 1.0
O G:LYS127 4.6 43.9 1.0
C G:LYS127 4.6 42.9 1.0
O G:HOH714 4.6 42.3 1.0
N G:PHE88 4.6 37.4 1.0
CA G:THR126 4.7 37.3 1.0
CB G:ASN87 4.8 36.3 1.0
CA G:ASN87 4.8 36.6 1.0
CA G:ASP125 4.9 34.5 1.0
C G:PHE88 5.0 39.7 1.0
CB G:SER255 5.0 35.2 1.0
C G:ASN87 5.0 37.6 1.0

Potassium binding site 8 out of 8 in 5scl

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Potassium 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 Potassium with other atoms in the K 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:K604

b:47.4
occ:1.00
 OD1 H:ASP125 2.5 40.5 1.0
O H:HOH885 2.6 49.7 1.0
OD1 H:ASN87 2.6 34.3 1.0
O H:THR126 2.7 38.8 1.0
OG H:SER89 2.9 39.0 1.0
CG H:ASP125 3.4 41.3 1.0
C H:THR126 3.6 39.6 1.0
OG H:SER255 3.7 33.7 1.0
CG H:ASN87 3.7 35.3 1.0
O H:ASP125 3.8 36.0 1.0
CB H:SER89 3.8 36.4 1.0
NZ H:LYS282 3.9 32.0 1.0
C H:ASP125 4.0 35.5 1.0
CB H:ASP125 4.1 34.4 1.0
N H:SER89 4.2 36.5 1.0
OD2 H:ASP125 4.2 46.2 1.0
N H:LYS127 4.3 40.6 1.0
NH2 H:ARG85 4.3 37.1 1.0
ND2 H:ASN87 4.3 36.0 1.0
CA H:LYS127 4.3 42.6 1.0
N H:THR126 4.4 36.3 1.0
O H:HOH743 4.5 39.1 1.0
CA H:SER89 4.6 36.4 1.0
CA H:THR126 4.6 38.0 1.0
CA H:ASP125 4.7 33.6 1.0
N H:PHE88 4.7 35.8 1.0
O H:LYS127 4.8 45.1 1.0
C H:LYS127 4.8 44.6 1.0
CB H:ASN87 4.8 33.7 1.0
CB H:SER255 4.9 33.4 1.0
CA H:ASN87 4.9 33.8 1.0
C H:ASN87 5.0 34.9 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: Wed Apr 5 09:38:28 2023

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