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Potassium in PDB 7fs3: Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15, PDB code: 7fs3 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) 189.21 / 1.66
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.686, 113.23, 189.296, 90, 91.71, 90
R / Rfree (%) 19.6 / 21.3

Other elements in 7fs3:

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15 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 15 (pdb code 7fs3). 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 15, PDB code: 7fs3:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 7fs3

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Potassium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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

b:56.9
occ:1.00
 OD1 A:ASP125 2.5 37.1 1.0
OD1 A:ASN87 2.6 40.9 1.0
O A:THR126 2.7 40.2 1.0
OG A:SER89 2.9 49.4 1.0
O A:HOH834 2.9 46.8 1.0
CG A:ASP125 3.4 37.8 1.0
C A:THR126 3.6 40.4 1.0
CG A:ASN87 3.7 40.5 1.0
OG A:SER255 3.7 36.7 1.0
O A:ASP125 3.7 34.6 1.0
NZ A:LYS282 3.9 33.0 1.0
CB A:SER89 4.0 46.7 1.0
C A:ASP125 4.0 34.9 1.0
CB A:ASP125 4.2 34.1 1.0
NH2 A:ARG85 4.2 34.1 1.0
N A:SER89 4.2 44.1 1.0
OD2 A:ASP125 4.3 40.7 1.0
N A:LYS127 4.3 42.1 1.0
CA A:LYS127 4.3 44.3 1.0
ND2 A:ASN87 4.3 41.7 1.0
N A:THR126 4.4 36.0 1.0
CA A:THR126 4.6 38.0 1.0
CA A:SER89 4.6 45.6 1.0
O A:HOH794 4.7 40.4 1.0
O A:LYS127 4.7 46.0 1.0
N A:PHE88 4.7 39.5 1.0
CA A:ASP125 4.7 33.6 1.0
O A:HOH910 4.7 58.2 1.0
C A:LYS127 4.8 46.1 1.0
CB A:ASN87 4.8 37.3 1.0
CA A:ASN87 4.9 36.5 1.0
CB A:SER255 4.9 34.7 1.0

Potassium binding site 2 out of 8 in 7fs3

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Potassium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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

b:50.1
occ:1.00
 OD1 B:ASN87 2.5 33.3 1.0
OD1 B:ASP125 2.6 35.2 1.0
OG B:SER89 2.8 42.6 1.0
O B:THR126 2.8 36.1 1.0
O B:HOH827 2.9 42.8 1.0
O B:HOH886 3.1 56.5 1.0
CG B:ASP125 3.6 34.9 1.0
CG B:ASN87 3.6 33.0 1.0
C B:THR126 3.7 36.6 1.0
OG B:SER255 3.8 33.2 1.0
O B:HOH898 3.8 57.7 1.0
CB B:SER89 3.8 40.6 1.0
O B:ASP125 3.8 31.7 1.0
NZ B:LYS282 4.0 32.4 1.0
N B:SER89 4.1 37.8 1.0
ND2 B:ASN87 4.1 34.0 1.0
C B:ASP125 4.2 31.3 1.0
NH2 B:ARG85 4.2 33.4 1.0
CB B:ASP125 4.3 30.6 1.0
CA B:LYS127 4.3 40.6 1.0
N B:LYS127 4.3 38.4 1.0
OD2 B:ASP125 4.4 36.6 1.0
N B:THR126 4.5 32.5 1.0
CA B:SER89 4.5 39.7 1.0
CA B:THR126 4.7 34.2 1.0
N B:PHE88 4.7 32.9 1.0
O B:LYS127 4.7 42.7 1.0
O B:HOH763 4.7 30.5 1.0
CB B:ASN87 4.7 30.6 1.0
C B:LYS127 4.8 42.4 1.0
CA B:ASN87 4.8 30.4 1.0
CA B:ASP125 4.9 29.8 1.0
C B:ASN87 5.0 31.6 1.0
CB B:SER255 5.0 31.8 1.0

Potassium binding site 3 out of 8 in 7fs3

Go back to Potassium Binding Sites List in 7fs3
Potassium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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

b:44.4
occ:1.00
 OD1 C:ASN87 2.6 28.3 1.0
OD1 C:ASP125 2.6 25.5 1.0
O C:HOH887 2.8 36.8 1.0
OG C:SER89 2.8 34.4 1.0
O C:THR126 2.8 22.5 1.0
O C:HOH986 3.0 44.5 1.0
CG C:ASP125 3.5 26.4 1.0
CG C:ASN87 3.6 27.4 1.0
C C:THR126 3.7 23.8 1.0
OG C:SER255 3.8 23.7 1.0
CB C:SER89 3.9 31.1 1.0
O C:ASP125 3.9 22.0 1.0
NZ C:LYS282 3.9 23.2 1.0
NH2 C:ARG85 4.1 29.9 1.0
ND2 C:ASN87 4.1 27.8 1.0
N C:SER89 4.2 27.6 1.0
C C:ASP125 4.2 21.1 1.0
CB C:ASP125 4.3 22.2 1.0
OD2 C:ASP125 4.3 28.8 1.0
O C:HOH895 4.3 48.0 1.0
CA C:LYS127 4.4 27.0 1.0
N C:LYS127 4.4 25.4 1.0
N C:THR126 4.5 21.1 1.0
CA C:SER89 4.6 29.9 1.0
O C:HOH800 4.6 28.1 1.0
CA C:THR126 4.7 22.2 1.0
N C:PHE88 4.7 23.8 1.0
O C:LYS127 4.7 29.1 1.0
CB C:ASN87 4.8 24.4 1.0
CA C:ASP125 4.9 20.7 1.0
C C:LYS127 4.9 28.8 1.0
CA C:ASN87 4.9 23.4 1.0

Potassium binding site 4 out of 8 in 7fs3

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Potassium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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

b:39.7
occ:1.00
 OD1 D:ASP125 2.6 25.6 1.0
O D:HOH908 2.6 35.4 1.0
O D:THR126 2.7 24.1 1.0
OD1 D:ASN87 2.7 21.7 1.0
OG D:SER89 2.8 28.6 1.0
O D:HOH965 2.8 47.9 1.0
CG D:ASP125 3.6 24.9 1.0
C D:THR126 3.6 25.2 1.0
OG D:SER255 3.7 23.6 1.0
CG D:ASN87 3.7 21.2 1.0
CB D:SER89 3.9 25.5 1.0
O D:ASP125 3.9 22.3 1.0
NZ D:LYS282 3.9 21.3 1.0
C D:ASP125 4.2 22.6 1.0
N D:SER89 4.2 23.8 1.0
CA D:LYS127 4.2 29.2 1.0
ND2 D:ASN87 4.2 23.5 1.0
N D:LYS127 4.3 26.9 1.0
NH2 D:ARG85 4.3 26.3 1.0
CB D:ASP125 4.4 21.1 1.0
OD2 D:ASP125 4.4 26.8 1.0
O D:HOH747 4.5 23.5 1.0
N D:THR126 4.5 23.0 1.0
CA D:SER89 4.6 24.6 1.0
O D:LYS127 4.6 31.6 1.0
CA D:THR126 4.6 24.0 1.0
C D:LYS127 4.7 31.6 1.0
O D:HOH955 4.7 36.6 1.0
N D:PHE88 4.8 21.0 1.0
CB D:SER255 4.9 22.3 1.0
CA D:ASP125 4.9 21.3 1.0
CB D:ASN87 4.9 20.6 1.0
CA D:ASN87 5.0 20.2 1.0

Potassium binding site 5 out of 8 in 7fs3

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Potassium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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

b:55.9
occ:1.00
 OD1 E:ASP125 2.4 35.1 1.0
O E:HOH801 2.7 35.7 1.0
O E:THR126 2.8 35.9 1.0
OD1 E:ASN87 2.9 33.1 1.0
O E:HOH925 3.0 36.1 1.0
OG E:SER89 3.1 45.2 1.0
CG E:ASP125 3.4 35.9 1.0
NZ E:LYS282 3.5 33.6 1.0
OG E:SER255 3.5 32.5 1.0
C E:THR126 3.8 36.8 1.0
CG E:ASN87 3.9 34.1 1.0
NH2 E:ARG85 4.0 33.0 1.0
O E:ASP125 4.1 33.4 1.0
OD2 E:ASP125 4.1 38.2 1.0
CB E:ASP125 4.2 32.8 1.0
O E:HOH766 4.2 29.9 1.0
CB E:SER89 4.2 40.7 1.0
C E:ASP125 4.2 33.5 1.0
ND2 E:ASN87 4.4 36.0 1.0
CA E:LYS127 4.5 40.1 1.0
N E:LYS127 4.5 38.1 1.0
N E:THR126 4.5 34.2 1.0
O E:HOH981 4.6 50.2 1.0
N E:SER89 4.6 37.2 1.0
O3 E:OXL602 4.7 29.6 1.0
O E:LYS127 4.7 42.1 1.0
CA E:THR126 4.7 35.2 1.0
O E:HOH791 4.8 30.1 1.0
CB E:SER255 4.8 31.4 1.0
CA E:ASP125 4.9 32.5 1.0
C E:LYS127 4.9 42.2 1.0
CE E:LYS282 5.0 32.6 1.0
CA E:SER89 5.0 38.0 1.0

Potassium binding site 6 out of 8 in 7fs3

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Potassium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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

b:58.1
occ:1.00
 OD1 F:ASP125 2.5 35.5 1.0
OD1 F:ASN87 2.5 32.8 1.0
O F:THR126 2.8 35.6 1.0
OG F:SER89 2.8 41.7 1.0
O F:HOH1001 2.9 53.4 1.0
O F:HOH796 3.0 41.3 1.0
CG F:ASP125 3.4 34.6 1.0
CG F:ASN87 3.6 32.7 1.0
C F:THR126 3.7 35.9 1.0
OG F:SER255 3.8 31.4 1.0
O F:ASP125 3.8 30.6 1.0
CB F:SER89 3.9 39.3 1.0
NZ F:LYS282 3.9 30.2 1.0
C F:ASP125 4.1 30.7 1.0
NH2 F:ARG85 4.1 32.9 1.0
ND2 F:ASN87 4.2 33.8 1.0
CB F:ASP125 4.2 30.4 1.0
N F:SER89 4.2 37.5 1.0
OD2 F:ASP125 4.2 35.5 1.0
N F:LYS127 4.4 37.1 1.0
CA F:LYS127 4.4 39.3 1.0
N F:THR126 4.5 32.0 1.0
CA F:SER89 4.6 39.0 1.0
O F:HOH897 4.6 48.7 1.0
O F:HOH752 4.6 31.6 1.0
CA F:THR126 4.7 33.8 1.0
N F:PHE88 4.7 33.3 1.0
CB F:ASN87 4.7 30.4 1.0
O F:LYS127 4.8 41.5 1.0
CA F:ASP125 4.8 29.2 1.0
CA F:ASN87 4.8 30.4 1.0
C F:LYS127 4.9 41.3 1.0
C F:ASN87 5.0 31.8 1.0

Potassium binding site 7 out of 8 in 7fs3

Go back to Potassium Binding Sites List in 7fs3
Potassium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K4006

b:41.8
occ:1.00
 OD1 G:ASP125 2.6 28.2 1.0
OD1 G:ASN87 2.6 23.7 1.0
O G:THR126 2.8 19.2 1.0
OG G:SER89 2.9 33.4 1.0
O G:HOH4294 2.9 37.7 1.0
O G:HOH4339 3.0 41.0 1.0
CG G:ASP125 3.5 25.9 1.0
CG G:ASN87 3.7 23.7 1.0
C G:THR126 3.7 20.7 1.0
OG G:SER255 3.8 23.2 1.0
NZ G:LYS282 3.9 22.0 1.0
O G:ASP125 3.9 20.7 1.0
CB G:SER89 3.9 29.8 1.0
NH2 G:ARG85 4.1 25.7 1.0
C G:ASP125 4.2 20.5 1.0
ND2 G:ASN87 4.2 24.3 1.0
OD2 G:ASP125 4.2 27.2 1.0
N G:SER89 4.3 25.9 1.0
CB G:ASP125 4.3 21.0 1.0
CA G:LYS127 4.3 25.2 1.0
N G:LYS127 4.4 22.4 1.0
O G:HOH4316 4.4 39.9 1.0
O G:HOH4388 4.5 49.8 1.0
N G:THR126 4.5 20.0 1.0
O G:HOH4143 4.6 25.7 1.0
CA G:SER89 4.6 28.0 1.0
O G:LYS127 4.7 29.0 1.0
CA G:THR126 4.7 20.6 1.0
N G:PHE88 4.8 21.2 1.0
CB G:ASN87 4.8 20.7 1.0
C G:LYS127 4.8 27.9 1.0
CA G:ASP125 4.9 18.9 1.0
CA G:ASN87 4.9 20.1 1.0
CB G:SER255 5.0 21.0 1.0

Potassium binding site 8 out of 8 in 7fs3

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Potassium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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

b:41.5
occ:1.00
 OD1 H:ASP125 2.6 24.1 1.0
OD1 H:ASN87 2.6 24.3 1.0
O H:THR126 2.7 22.6 1.0
OG H:SER89 2.8 31.6 1.0
O H:HOH827 2.8 32.9 1.0
O H:HOH980 2.8 45.7 1.0
CG H:ASP125 3.5 23.6 1.0
CG H:ASN87 3.6 24.3 1.0
C H:THR126 3.7 22.9 1.0
OG H:SER255 3.7 23.1 1.0
O H:ASP125 3.8 19.8 1.0
CB H:SER89 3.8 28.8 1.0
NZ H:LYS282 3.9 24.1 1.0
C H:ASP125 4.1 19.4 1.0
N H:SER89 4.1 25.4 1.0
ND2 H:ASN87 4.2 25.3 1.0
NH2 H:ARG85 4.2 23.7 1.0
CB H:ASP125 4.2 18.9 1.0
OD2 H:ASP125 4.3 24.6 1.0
CA H:LYS127 4.3 26.6 1.0
N H:LYS127 4.3 24.4 1.0
O H:HOH897 4.3 42.6 1.0
N H:THR126 4.5 19.9 1.0
O H:HOH772 4.5 25.2 1.0
CA H:SER89 4.5 27.7 1.0
CA H:THR126 4.6 21.1 1.0
N H:PHE88 4.7 21.5 1.0
O H:LYS127 4.7 29.5 1.0
CA H:ASP125 4.8 18.1 1.0
CB H:ASN87 4.8 21.2 1.0
C H:LYS127 4.8 28.8 1.0
CA H:ASN87 4.9 20.6 1.0
CB H:SER255 5.0 22.1 1.0
C H:ASN87 5.0 21.1 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 19:00:12 2024

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