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Potassium in PDB 5scj: Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106, PDB code: 5scj 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) 188.89 / 2.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.143, 113.061, 188.959, 90, 91.54, 90
R / Rfree (%) 21.8 / 25.3

Other elements in 5scj:

The structure of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106 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 106 (pdb code 5scj). 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 106, PDB code: 5scj:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 5scj

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Potassium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106


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 106 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:101.2
occ:1.00
O A:THR126 2.4 89.0 1.0
OG A:SER89 2.7 92.5 1.0
OD1 A:ASN87 2.8 88.3 1.0
OD1 A:ASP125 2.9 93.2 1.0
OG A:SER255 3.4 88.0 1.0
C A:THR126 3.4 88.7 1.0
O6 A:I9K605 3.6 130.6 1.0
CB A:SER89 3.7 90.0 1.0
CA A:LYS127 3.7 91.5 1.0
N A:LYS127 4.0 90.0 1.0
CG A:ASP125 4.0 91.6 1.0
CG A:ASN87 4.0 87.0 1.0
NZ A:LYS282 4.0 77.7 1.0
O A:ASP125 4.1 84.1 1.0
O A:LYS127 4.1 92.5 1.0
C A:LYS127 4.2 92.4 1.0
N A:SER89 4.2 87.6 1.0
C A:ASP125 4.4 84.2 1.0
C19 A:I9K605 4.4 130.4 1.0
CA A:SER89 4.5 88.8 1.0
ND2 A:ASN87 4.5 87.5 1.0
CB A:SER255 4.5 84.9 1.0
CA A:THR126 4.6 86.7 1.0
N A:THR126 4.6 85.2 1.0
CB A:ASP125 4.7 85.7 1.0
O5 A:I9K605 4.7 130.3 1.0
H11 A:I9K605 4.7 130.5 0.0
NH2 A:ARG85 4.8 86.9 1.0
OD2 A:ASP125 4.8 93.4 1.0
CB A:LYS127 5.0 94.1 1.0

Potassium binding site 2 out of 8 in 5scj

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Potassium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106


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 106 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K604

b:81.0
occ:1.00
OD1 B:ASN87 2.6 61.4 1.0
OG B:SER89 2.7 74.4 1.0
OD1 B:ASP125 2.8 71.1 1.0
O B:THR126 2.9 66.9 1.0
CB B:SER89 3.6 72.4 1.0
CG B:ASN87 3.6 61.4 1.0
OG B:SER255 3.7 50.5 1.0
CG B:ASP125 3.8 70.0 1.0
NZ B:LYS282 3.9 58.6 1.0
C B:THR126 3.9 66.3 1.0
ND2 B:ASN87 4.1 61.8 1.0
O B:ASP125 4.2 59.6 1.0
CA B:LYS127 4.3 70.2 1.0
N B:SER89 4.3 69.7 1.0
NH2 B:ARG85 4.3 54.1 1.0
N B:LYS127 4.5 67.9 1.0
CA B:SER89 4.5 71.3 1.0
CB B:ASP125 4.5 63.7 1.0
C B:ASP125 4.5 60.7 1.0
O B:LYS127 4.6 73.1 1.0
OD2 B:ASP125 4.6 72.6 1.0
C B:LYS127 4.7 72.6 1.0
CB B:SER255 4.9 51.0 1.0
N B:THR126 4.9 62.1 1.0
CB B:ASN87 4.9 61.1 1.0
O4 B:OXL602 4.9 49.7 1.0

Potassium binding site 3 out of 8 in 5scj

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Potassium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106


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 106 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K604

b:77.2
occ:1.00
OD1 C:ASN87 2.4 56.4 1.0
O C:HOH764 2.5 66.0 1.0
OD1 C:ASP125 2.7 55.9 1.0
O C:THR126 2.8 54.5 1.0
OG C:SER89 2.8 56.4 1.0
CG C:ASN87 3.5 56.5 1.0
CB C:SER89 3.6 54.5 1.0
CG C:ASP125 3.6 55.0 1.0
C C:THR126 3.7 55.5 1.0
OG C:SER255 3.7 49.0 1.0
O C:ASP125 3.9 51.8 1.0
ND2 C:ASN87 4.0 58.5 1.0
NZ C:LYS282 4.0 44.5 1.0
N C:SER89 4.0 52.8 1.0
CA C:LYS127 4.2 59.9 1.0
C C:ASP125 4.2 52.6 1.0
CB C:ASP125 4.3 51.9 1.0
O4 C:I9K605 4.3 97.8 1.0
N C:LYS127 4.3 57.3 1.0
NH2 C:ARG85 4.3 59.7 1.0
CA C:SER89 4.4 53.5 1.0
OD2 C:ASP125 4.5 57.6 1.0
N C:THR126 4.6 53.7 1.0
CB C:ASN87 4.7 53.4 1.0
O C:LYS127 4.7 61.3 1.0
N C:PHE88 4.7 52.2 1.0
CA C:THR126 4.8 54.2 1.0
C C:LYS127 4.8 61.3 1.0
O C:HOH744 4.8 79.2 1.0
CA C:ASN87 4.8 53.1 1.0
CA C:ASP125 4.9 51.6 1.0
CB C:SER255 4.9 47.5 1.0
C C:ASN87 5.0 53.4 1.0
C C:PHE88 5.0 53.1 1.0
O4 C:OXL602 5.0 54.1 1.0

Potassium binding site 4 out of 8 in 5scj

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Potassium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106


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 106 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K604

b:67.2
occ:1.00
OD1 D:ASP125 2.5 45.0 1.0
O D:THR126 2.7 43.9 1.0
OD1 D:ASN87 2.7 38.6 1.0
OG D:SER89 3.0 46.2 1.0
CG D:ASP125 3.4 42.7 1.0
C D:THR126 3.6 43.7 1.0
O D:ASP125 3.6 38.9 1.0
CG D:ASN87 3.7 36.9 1.0
OG D:SER255 3.8 37.5 1.0
CB D:SER89 3.9 41.9 1.0
C D:ASP125 3.9 38.5 1.0
CB D:ASP125 4.0 38.2 1.0
NZ D:LYS282 4.0 41.4 1.0
N D:SER89 4.1 38.8 1.0
CA D:LYS127 4.2 48.2 1.0
NH2 D:ARG85 4.2 41.3 1.0
N D:LYS127 4.2 45.7 1.0
ND2 D:ASN87 4.3 38.3 1.0
OD2 D:ASP125 4.3 43.7 1.0
N D:THR126 4.4 39.4 1.0
N D:PHE88 4.4 34.0 1.0
CA D:SER89 4.5 40.8 1.0
CA D:THR126 4.6 41.1 1.0
CA D:ASP125 4.6 36.8 1.0
CB D:ASN87 4.8 32.2 1.0
CA D:ASN87 4.8 31.8 1.0
O D:LYS127 4.8 52.7 1.0
C D:LYS127 4.8 51.8 1.0
C D:ASN87 4.9 33.5 1.0
C D:PHE88 4.9 37.2 1.0

Potassium binding site 5 out of 8 in 5scj

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Potassium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106


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 106 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K604

b:113.9
occ:1.00
O E:THR126 2.5 78.7 1.0
OG E:SER89 2.7 87.9 1.0
OD1 E:ASN87 2.8 79.3 1.0
OD1 E:ASP125 2.8 83.1 1.0
OG E:SER255 3.5 69.7 1.0
C E:THR126 3.5 78.8 1.0
CB E:SER89 3.6 84.7 1.0
CG E:ASP125 3.8 82.2 1.0
CA E:LYS127 3.9 82.5 1.0
CG E:ASN87 3.9 78.6 1.0
NZ E:LYS282 3.9 63.6 1.0
O E:ASP125 4.0 76.3 1.0
N E:LYS127 4.1 80.5 1.0
N E:SER89 4.2 81.2 1.0
O E:LYS127 4.2 84.4 1.0
C E:ASP125 4.3 76.4 1.0
C E:LYS127 4.3 84.1 1.0
ND2 E:ASN87 4.4 79.3 1.0
CA E:SER89 4.4 83.0 1.0
CB E:ASP125 4.5 78.0 1.0
N E:THR126 4.6 76.5 1.0
CA E:THR126 4.6 77.2 1.0
CB E:SER255 4.6 68.3 1.0
NH2 E:ARG85 4.7 68.7 1.0
OD2 E:ASP125 4.7 83.9 1.0
N E:PHE88 4.9 77.8 1.0

Potassium binding site 6 out of 8 in 5scj

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Potassium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106


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 106 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K604

b:79.5
occ:1.00
OD1 F:ASN87 2.5 50.4 1.0
OG F:SER89 2.7 60.9 1.0
O F:THR126 2.7 57.9 1.0
OD1 F:ASP125 2.8 63.1 1.0
CB F:SER89 3.5 60.0 1.0
C F:THR126 3.7 57.6 1.0
CG F:ASN87 3.7 49.7 1.0
OG F:SER255 3.8 44.5 1.0
CG F:ASP125 3.8 61.4 1.0
O F:ASP125 4.0 51.7 1.0
NZ F:LYS282 4.0 55.7 1.0
N F:SER89 4.0 60.2 1.0
CA F:LYS127 4.1 61.1 1.0
O5 F:I9K605 4.2 89.9 1.0
N F:LYS127 4.2 59.3 1.0
H11 F:I9K605 4.3 86.9 0.0
ND2 F:ASN87 4.3 49.0 1.0
H14 F:I9K605 4.3 88.3 0.0
CA F:SER89 4.3 60.4 1.0
C F:ASP125 4.3 52.6 1.0
NH2 F:ARG85 4.4 50.2 1.0
H15 F:I9K605 4.4 89.9 0.0
CB F:ASP125 4.4 55.4 1.0
O F:LYS127 4.5 63.0 1.0
C F:LYS127 4.6 62.5 1.0
OD2 F:ASP125 4.6 63.0 1.0
N F:THR126 4.7 53.2 1.0
O2 F:I9K605 4.7 86.9 1.0
N F:PHE88 4.8 56.9 1.0
CA F:THR126 4.8 55.0 1.0
C19 F:I9K605 4.9 89.6 1.0
CB F:ASN87 4.9 50.3 1.0
CB F:SER255 5.0 44.6 1.0
C F:PHE88 5.0 60.4 1.0
CA F:ASN87 5.0 52.1 1.0

Potassium binding site 7 out of 8 in 5scj

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Potassium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106


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 106 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K604

b:65.1
occ:1.00
O G:THR126 2.6 52.5 1.0
OD1 G:ASN87 2.6 45.1 1.0
OD1 G:ASP125 2.7 52.2 1.0
OG G:SER89 2.7 52.7 1.0
OG G:SER255 3.6 45.2 1.0
C G:THR126 3.6 52.0 1.0
CB G:SER89 3.7 51.3 1.0
CG G:ASN87 3.7 43.5 1.0
CG G:ASP125 3.7 51.9 1.0
NZ G:LYS282 3.9 44.8 1.0
O G:ASP125 4.0 49.7 1.0
CA G:LYS127 4.0 55.5 1.0
N G:LYS127 4.2 53.1 1.0
ND2 G:ASN87 4.2 43.2 1.0
N G:SER89 4.2 49.2 1.0
C G:ASP125 4.3 48.3 1.0
O4 G:I9K605 4.4 92.9 1.0
CB G:ASP125 4.4 47.4 1.0
O G:LYS127 4.4 57.0 1.0
CA G:SER89 4.5 50.0 1.0
NH2 G:ARG85 4.5 64.2 1.0
C G:LYS127 4.5 57.0 1.0
O6 G:I9K605 4.5 94.5 1.0
OD2 G:ASP125 4.6 54.6 1.0
N G:THR126 4.6 48.2 1.0
CA G:THR126 4.7 49.3 1.0
CB G:SER255 4.7 44.2 1.0
N G:PHE88 4.9 45.0 1.0
CB G:ASN87 4.9 42.3 1.0
CA G:ASP125 5.0 46.4 1.0

Potassium binding site 8 out of 8 in 5scj

Go back to Potassium Binding Sites List in 5scj
Potassium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 106


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 106 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K604

b:73.8
occ:1.00
OD1 H:ASP125 2.6 45.7 1.0
O H:THR126 2.6 44.8 1.0
OD1 H:ASN87 2.8 44.3 1.0
OG H:SER89 2.9 53.9 1.0
OG H:SER255 3.3 37.8 1.0
C H:THR126 3.6 45.0 1.0
CG H:ASP125 3.6 44.1 1.0
NZ H:LYS282 3.7 43.7 1.0
CB H:SER89 3.9 50.5 1.0
CG H:ASN87 3.9 42.2 1.0
O H:ASP125 4.1 39.9 1.0
CA H:LYS127 4.1 50.5 1.0
N H:LYS127 4.2 47.5 1.0
C H:ASP125 4.3 40.0 1.0
ND2 H:ASN87 4.4 43.4 1.0
N H:SER89 4.4 46.2 1.0
CB H:ASP125 4.4 39.5 1.0
O H:LYS127 4.4 52.8 1.0
OD2 H:ASP125 4.4 45.8 1.0
NH2 H:ARG85 4.4 42.5 1.0
C H:LYS127 4.5 53.2 1.0
CB H:SER255 4.5 37.1 1.0
N H:THR126 4.6 40.9 1.0
CA H:SER89 4.7 48.4 1.0
CA H:THR126 4.7 42.5 1.0
O H:HOH835 4.9 43.3 1.0
CA H:ASP125 4.9 38.7 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: Wed Apr 5 09:38:28 2023

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