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Potassium in PDB 7frx: Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5, PDB code: 7frx was solved by A.Lulla, O.Nilsson, P.Brear, A.Nain-Perez, M.Grotli, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 189.12 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.844, 113.199, 189.15, 90, 90.99, 90
R / Rfree (%) 20 / 22.2

Other elements in 7frx:

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

Potassium binding site 1 out of 8 in 7frx

Go back to Potassium Binding Sites List in 7frx
Potassium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 Allosteric Modulator 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:71.5
occ:1.00
 OD1 A:ASN87 2.6 52.7 1.0
OG A:SER89 2.6 65.0 1.0
OD1 A:ASP125 2.7 53.1 1.0
O A:THR126 2.8 55.2 1.0
O A:HOH822 2.8 55.9 1.0
C A:THR126 3.6 55.6 1.0
CG A:ASP125 3.6 53.0 1.0
O A:ASP125 3.6 51.2 1.0
CB A:SER89 3.8 62.3 1.0
CG A:ASN87 3.8 52.7 1.0
OG A:SER255 3.9 52.2 1.0
C A:ASP125 4.0 51.1 1.0
N A:SER89 4.0 59.4 1.0
N A:LYS127 4.1 57.1 1.0
CA A:LYS127 4.2 58.9 1.0
NZ A:LYS282 4.2 47.3 1.0
CB A:ASP125 4.2 50.1 1.0
NH2 A:ARG85 4.3 47.7 1.0
N A:THR126 4.4 52.0 1.0
OD2 A:ASP125 4.4 55.0 1.0
CA A:SER89 4.4 60.7 1.0
N A:PHE88 4.5 55.3 1.0
CA A:THR126 4.5 53.6 1.0
ND2 A:ASN87 4.6 53.0 1.0
O A:LYS127 4.7 60.9 1.0
CA A:ASP125 4.7 49.6 1.0
C A:LYS127 4.7 60.7 1.0
CA A:ASN87 4.7 52.1 1.0
O A:HOH852 4.8 58.0 1.0
O A:HOH753 4.8 43.7 1.0
CB A:ASN87 4.8 52.0 1.0
C A:ASN87 4.8 54.2 1.0
C A:PHE88 4.9 58.5 1.0

Potassium binding site 2 out of 8 in 7frx

Go back to Potassium Binding Sites List in 7frx
Potassium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 Allosteric Modulator 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K604

b:74.6
occ:1.00
 OD1 B:ASN87 2.7 48.0 1.0
OG B:SER89 2.7 58.7 1.0
O B:HOH780 2.8 54.3 1.0
OD1 B:ASP125 2.8 45.8 1.0
O B:THR126 2.9 50.6 1.0
CG B:ASP125 3.7 45.5 1.0
CG B:ASN87 3.7 47.5 1.0
CB B:SER89 3.8 56.3 1.0
OG B:SER255 3.8 42.4 1.0
C B:THR126 3.8 50.3 1.0
NZ B:LYS282 3.9 38.5 1.0
O B:ASP125 4.0 43.2 1.0
NH2 B:ARG85 4.2 40.5 1.0
ND2 B:ASN87 4.2 47.9 1.0
N B:SER89 4.3 53.3 1.0
CA B:LYS127 4.3 54.8 1.0
C B:ASP125 4.4 43.2 1.0
N B:LYS127 4.4 52.3 1.0
OD2 B:ASP125 4.4 47.8 1.0
CB B:ASP125 4.5 41.5 1.0
O B:LYS127 4.6 56.9 1.0
CA B:SER89 4.6 54.8 1.0
N B:THR126 4.7 45.2 1.0
C B:LYS127 4.8 56.7 1.0
CA B:THR126 4.9 47.6 1.0
N B:PHE88 4.9 47.9 1.0
CB B:ASN87 4.9 45.5 1.0
CB B:SER255 5.0 39.6 1.0

Potassium binding site 3 out of 8 in 7frx

Go back to Potassium Binding Sites List in 7frx
Potassium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 Allosteric Modulator 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K604

b:52.7
occ:1.00
 OD1 C:ASN87 2.4 32.4 1.0
OD1 C:ASP125 2.7 33.5 1.0
OG C:SER89 2.8 40.2 1.0
O C:HOH896 2.8 50.5 1.0
O C:THR126 2.9 27.4 1.0
O C:HOH921 3.1 35.5 1.0
CG C:ASN87 3.5 33.2 1.0
CG C:ASP125 3.5 32.5 1.0
O C:ASP125 3.8 27.2 1.0
CB C:SER89 3.8 36.6 1.0
C C:THR126 3.8 28.9 1.0
OG C:SER255 3.9 30.0 1.0
ND2 C:ASN87 4.0 33.8 1.0
NZ C:LYS282 4.1 27.4 1.0
N C:SER89 4.1 32.9 1.0
NH2 C:ARG85 4.1 34.9 1.0
C C:ASP125 4.1 26.6 1.0
CB C:ASP125 4.2 27.2 1.0
OD2 C:ASP125 4.3 34.7 1.0
CA C:LYS127 4.4 33.0 1.0
N C:LYS127 4.4 30.9 1.0
O C:HOH882 4.4 57.3 1.0
CA C:SER89 4.5 34.9 1.0
N C:THR126 4.6 26.6 1.0
N C:PHE88 4.6 29.2 1.0
CB C:ASN87 4.6 30.5 1.0
O C:HOH750 4.6 33.5 1.0
CA C:ASN87 4.7 29.8 1.0
CA C:THR126 4.7 27.2 1.0
O C:LYS127 4.8 34.5 1.0
CA C:ASP125 4.8 26.3 1.0
C C:ASN87 4.9 29.8 1.0
C C:LYS127 4.9 34.3 1.0

Potassium binding site 4 out of 8 in 7frx

Go back to Potassium Binding Sites List in 7frx
Potassium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 Allosteric Modulator 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K604

b:46.9
occ:1.00
 OD1 D:ASP125 2.6 27.9 1.0
OD1 D:ASN87 2.6 28.0 1.0
O D:THR126 2.7 28.9 1.0
OG D:SER89 2.9 36.1 1.0
O D:HOH872 2.9 42.0 1.0
O D:HOH950 2.9 52.3 1.0
CG D:ASP125 3.5 26.9 1.0
C D:THR126 3.6 29.6 1.0
CG D:ASN87 3.6 26.9 1.0
O D:ASP125 3.7 27.6 1.0
OG D:SER255 3.8 29.0 1.0
CB D:SER89 3.9 32.4 1.0
NZ D:LYS282 3.9 29.2 1.0
C D:ASP125 4.0 26.6 1.0
ND2 D:ASN87 4.2 27.7 1.0
N D:SER89 4.2 29.3 1.0
NH2 D:ARG85 4.2 26.7 1.0
CB D:ASP125 4.2 24.0 1.0
CA D:LYS127 4.2 34.4 1.0
N D:LYS127 4.2 31.3 1.0
OD2 D:ASP125 4.3 27.7 1.0
N D:THR126 4.4 26.3 1.0
CA D:THR126 4.6 27.5 1.0
O D:HOH968 4.6 43.3 1.0
CA D:SER89 4.6 30.9 1.0
N D:PHE88 4.6 25.1 1.0
O D:LYS127 4.7 37.8 1.0
CA D:ASP125 4.7 24.4 1.0
C D:LYS127 4.8 37.1 1.0
CB D:ASN87 4.8 24.0 1.0
CA D:ASN87 4.8 23.6 1.0
C D:ASN87 4.9 24.8 1.0
CB D:SER255 5.0 28.6 1.0

Potassium binding site 5 out of 8 in 7frx

Go back to Potassium Binding Sites List in 7frx
Potassium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 Allosteric Modulator 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K604

b:77.5
occ:1.00
 OD1 E:ASN87 2.6 46.6 1.0
OD1 E:ASP125 2.6 55.2 1.0
O E:THR126 2.7 56.2 1.0
OG E:SER89 2.8 60.3 1.0
O E:HOH887 3.3 58.6 1.0
CG E:ASP125 3.6 54.8 1.0
C E:THR126 3.6 56.2 1.0
CG E:ASN87 3.7 46.3 1.0
OG E:SER255 3.7 45.3 1.0
O E:ASP125 3.7 51.1 1.0
CB E:SER89 3.9 57.6 1.0
NZ E:LYS282 4.0 45.6 1.0
C E:ASP125 4.1 51.1 1.0
N E:SER89 4.2 54.6 1.0
CA E:LYS127 4.2 59.5 1.0
N E:LYS127 4.2 57.7 1.0
NH2 E:ARG85 4.2 42.3 1.0
CB E:ASP125 4.3 51.1 1.0
ND2 E:ASN87 4.3 46.2 1.0
OD2 E:ASP125 4.4 56.5 1.0
N E:THR126 4.5 52.3 1.0
CA E:SER89 4.5 56.2 1.0
CA E:THR126 4.6 53.9 1.0
O E:LYS127 4.6 61.1 1.0
N E:PHE88 4.7 48.9 1.0
C E:LYS127 4.7 61.2 1.0
CA E:ASP125 4.8 49.4 1.0
CB E:ASN87 4.8 44.7 1.0
CA E:ASN87 4.9 44.7 1.0
CB E:SER255 4.9 45.3 1.0
C E:ASN87 5.0 47.2 1.0

Potassium binding site 6 out of 8 in 7frx

Go back to Potassium Binding Sites List in 7frx
Potassium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 Allosteric Modulator 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K604

b:71.7
occ:1.00
 OD1 F:ASP125 2.6 45.5 1.0
O F:THR126 2.7 44.1 1.0
OD1 F:ASN87 2.7 41.4 1.0
OG F:SER89 2.8 50.7 1.0
CG F:ASP125 3.6 43.9 1.0
C F:THR126 3.6 44.5 1.0
OG F:SER255 3.7 37.7 1.0
O F:ASP125 3.8 38.1 1.0
CG F:ASN87 3.8 40.5 1.0
NZ F:LYS282 3.9 33.2 1.0
CB F:SER89 3.9 49.1 1.0
C F:ASP125 4.1 38.5 1.0
CA F:LYS127 4.2 49.4 1.0
N F:SER89 4.2 47.4 1.0
N F:LYS127 4.2 46.6 1.0
NH2 F:ARG85 4.2 38.6 1.0
CB F:ASP125 4.3 38.5 1.0
OD2 F:ASP125 4.4 46.0 1.0
ND2 F:ASN87 4.4 40.5 1.0
N F:THR126 4.5 40.1 1.0
O F:LYS127 4.5 52.1 1.0
O F:HOH744 4.6 38.6 1.0
O F:HOH892 4.6 49.1 1.0
CA F:SER89 4.6 48.7 1.0
CA F:THR126 4.6 42.1 1.0
C F:LYS127 4.7 51.5 1.0
N F:PHE88 4.8 41.8 1.0
CA F:ASP125 4.8 37.4 1.0
CB F:SER255 4.9 35.4 1.0
CB F:ASN87 4.9 38.7 1.0
CA F:ASN87 5.0 38.1 1.0

Potassium binding site 7 out of 8 in 7frx

Go back to Potassium Binding Sites List in 7frx
Potassium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 Allosteric Modulator 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K604

b:50.2
occ:1.00
 OD1 G:ASN87 2.6 31.8 1.0
OD1 G:ASP125 2.6 29.7 1.0
O G:HOH920 2.7 41.1 1.0
OG G:SER89 2.8 40.9 1.0
O G:THR126 2.9 28.9 1.0
O G:HOH859 2.9 39.0 1.0
CG G:ASP125 3.5 28.7 1.0
CG G:ASN87 3.6 31.0 1.0
C G:THR126 3.8 29.7 1.0
OG G:SER255 3.8 28.6 1.0
O G:ASP125 3.9 26.0 1.0
NZ G:LYS282 3.9 28.0 1.0
CB G:SER89 3.9 36.8 1.0
NH2 G:ARG85 4.1 33.2 1.0
ND2 G:ASN87 4.2 31.7 1.0
C G:ASP125 4.2 26.1 1.0
N G:SER89 4.2 31.8 1.0
CB G:ASP125 4.3 25.0 1.0
OD2 G:ASP125 4.3 29.9 1.0
CA G:LYS127 4.4 33.2 1.0
O G:HOH905 4.4 47.2 1.0
N G:LYS127 4.4 31.2 1.0
O G:HOH910 4.5 69.2 1.0
N G:THR126 4.6 26.4 1.0
O G:HOH827 4.6 37.1 1.0
CA G:SER89 4.6 34.7 1.0
O G:LYS127 4.7 34.5 1.0
CA G:THR126 4.7 27.8 1.0
N G:PHE88 4.8 27.9 1.0
CB G:ASN87 4.8 28.0 1.0
C G:LYS127 4.8 34.3 1.0
CA G:ASP125 4.9 24.2 1.0
CA G:ASN87 4.9 27.2 1.0
CB G:SER255 5.0 27.1 1.0

Potassium binding site 8 out of 8 in 7frx

Go back to Potassium Binding Sites List in 7frx
Potassium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 5


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 Allosteric Modulator 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K604

b:48.7
occ:1.00
 OD1 H:ASN87 2.5 27.3 1.0
OD1 H:ASP125 2.5 28.2 1.0
O H:THR126 2.8 24.6 1.0
O H:HOH963 2.8 43.9 1.0
OG H:SER89 2.9 37.1 1.0
CG H:ASP125 3.5 27.7 1.0
CG H:ASN87 3.6 25.4 1.0
C H:THR126 3.6 26.2 1.0
O H:ASP125 3.6 25.1 1.0
OG H:SER255 3.8 27.5 1.0
NZ H:LYS282 3.9 24.4 1.0
CB H:SER89 3.9 34.2 1.0
C H:ASP125 4.0 24.2 1.0
N H:SER89 4.1 30.2 1.0
CB H:ASP125 4.2 23.7 1.0
NH2 H:ARG85 4.2 26.6 1.0
ND2 H:ASN87 4.2 25.3 1.0
OD2 H:ASP125 4.3 30.3 1.0
N H:LYS127 4.3 28.8 1.0
CA H:LYS127 4.3 32.1 1.0
N H:THR126 4.4 24.3 1.0
O H:HOH744 4.4 64.9 1.0
O H:HOH966 4.5 46.0 1.0
CA H:SER89 4.6 33.0 1.0
N H:PHE88 4.6 25.4 1.0
CA H:THR126 4.6 25.2 1.0
O H:HOH777 4.6 30.3 1.0
O H:LYS127 4.7 34.5 1.0
CA H:ASP125 4.7 22.4 1.0
CB H:ASN87 4.7 23.5 1.0
CA H:ASN87 4.8 23.1 1.0
C H:LYS127 4.8 34.6 1.0
C H:ASN87 4.9 24.4 1.0
CB H:SER255 5.0 26.7 1.0

Reference:

A.Nain-Perez, O.Nilsson, A.Lulla, L.Haversen, P.Brear, S.Liljenberg, M.Hyvonen, J.Boren, M.Grotli. Tuning Liver Pyruvate Kinase Activity Up or Down with A New Class of Allosteric Modulators. Eur.J.Med.Chem. V. 250 15177 2023.
ISSN: ISSN 0223-5234
PubMed: 36753880
DOI: 10.1016/J.EJMECH.2023.115177
Page generated: Mon Aug 12 18:56:13 2024

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