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Potassium in PDB 7frw: Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4, PDB code: 7frw 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) 104.04 / 1.74
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.144, 112.752, 188.438, 90, 91.41, 90
R / Rfree (%) 20.2 / 22

Other elements in 7frw:

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

Potassium binding site 1 out of 8 in 7frw

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Potassium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:77.4
occ:1.00
 OD1 A:ASN87 2.5 60.6 1.0
OD1 A:ASP125 2.6 62.1 1.0
O A:THR126 2.7 61.9 1.0
OG A:SER89 2.8 69.7 1.0
C A:THR126 3.5 62.1 1.0
O A:ASP125 3.5 57.1 1.0
CG A:ASP125 3.6 61.6 1.0
CG A:ASN87 3.7 60.2 1.0
CB A:SER89 3.9 67.9 1.0
C A:ASP125 3.9 57.1 1.0
N A:SER89 4.0 65.5 1.0
OG A:SER255 4.0 56.6 1.0
NZ A:LYS282 4.1 54.8 1.0
CB A:ASP125 4.1 57.4 1.0
N A:LYS127 4.1 63.8 1.0
CA A:LYS127 4.2 65.9 1.0
NH2 A:ARG85 4.3 53.0 1.0
N A:THR126 4.3 58.1 1.0
ND2 A:ASN87 4.3 61.1 1.0
N A:PHE88 4.4 61.0 1.0
OD2 A:ASP125 4.4 63.8 1.0
CA A:THR126 4.5 60.0 1.0
CA A:SER89 4.5 66.9 1.0
O A:LYS127 4.7 67.5 1.0
CA A:ASP125 4.7 55.6 1.0
CA A:ASN87 4.7 57.7 1.0
CB A:ASN87 4.7 58.4 1.0
C A:LYS127 4.7 67.4 1.0
C A:ASN87 4.8 59.7 1.0
C A:PHE88 4.8 64.6 1.0

Potassium binding site 2 out of 8 in 7frw

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Potassium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:78.0
occ:1.00
 O B:HOH831 2.4 53.0 1.0
OD1 B:ASN87 2.5 58.4 1.0
OG B:SER89 2.7 71.2 1.0
O B:THR126 2.8 66.0 1.0
OD1 B:ASP125 2.8 63.5 1.0
CG B:ASN87 3.6 58.5 1.0
C B:THR126 3.7 65.7 1.0
CB B:SER89 3.7 69.0 1.0
CG B:ASP125 3.7 63.7 1.0
O B:HOH893 3.7 78.7 1.0
O B:ASP125 3.8 59.1 1.0
N B:SER89 4.0 66.0 1.0
OG B:SER255 4.1 52.4 1.0
NZ B:LYS282 4.1 50.0 1.0
C B:ASP125 4.2 59.4 1.0
CA B:LYS127 4.2 70.0 1.0
ND2 B:ASN87 4.2 59.8 1.0
NH2 B:ARG85 4.2 50.5 1.0
N B:LYS127 4.3 67.6 1.0
CB B:ASP125 4.3 59.4 1.0
CA B:SER89 4.4 67.6 1.0
OD2 B:ASP125 4.6 66.4 1.0
N B:THR126 4.6 60.9 1.0
N B:PHE88 4.6 60.6 1.0
O B:LYS127 4.6 72.0 1.0
CA B:THR126 4.7 63.0 1.0
C B:LYS127 4.7 71.9 1.0
CB B:ASN87 4.8 56.6 1.0
CA B:ASN87 4.8 56.2 1.0
C B:ASN87 4.9 58.7 1.0
CA B:ASP125 4.9 57.9 1.0
C B:PHE88 4.9 64.9 1.0

Potassium binding site 3 out of 8 in 7frw

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Potassium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K605

b:49.8
occ:1.00
 OD1 C:ASN87 2.4 39.1 1.0
OD1 C:ASP125 2.7 41.0 1.0
OG C:SER89 2.7 41.2 1.0
O C:THR126 2.8 33.0 1.0
O C:HOH906 3.0 53.8 1.0
O C:HOH763 3.4 94.0 1.0
CG C:ASN87 3.6 39.2 1.0
CG C:ASP125 3.6 39.2 1.0
C C:THR126 3.7 33.8 1.0
O C:ASP125 3.7 32.6 1.0
CB C:SER89 3.8 39.7 1.0
N C:SER89 4.0 37.8 1.0
OG C:SER255 4.0 37.8 1.0
C C:ASP125 4.0 32.1 1.0
NZ C:LYS282 4.1 36.5 1.0
NH2 C:ARG85 4.2 40.3 1.0
CB C:ASP125 4.2 32.9 1.0
ND2 C:ASN87 4.2 40.5 1.0
CA C:LYS127 4.3 37.7 1.0
N C:LYS127 4.3 35.4 1.0
CA C:SER89 4.4 39.6 1.0
OD2 C:ASP125 4.5 41.8 1.0
N C:THR126 4.5 32.2 1.0
N C:PHE88 4.5 34.6 1.0
CA C:THR126 4.6 32.3 1.0
CB C:ASN87 4.7 36.2 1.0
CA C:ASN87 4.7 34.8 1.0
O C:LYS127 4.7 40.4 1.0
O C:HOH934 4.7 65.0 1.0
CA C:ASP125 4.8 31.0 1.0
C C:ASN87 4.8 34.8 1.0
C C:LYS127 4.8 39.5 1.0
C C:PHE88 4.9 36.9 1.0
O C:HOH743 5.0 41.9 1.0

Potassium binding site 4 out of 8 in 7frw

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


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

b:43.1
occ:1.00
 OD1 D:ASN87 2.6 29.8 1.0
OD1 D:ASP125 2.7 32.4 1.0
O D:THR126 2.7 31.9 1.0
OG D:SER89 2.8 33.8 1.0
O D:HOH798 2.9 55.2 1.0
O D:HOH831 3.0 37.1 1.0
C D:THR126 3.6 32.2 1.0
CG D:ASP125 3.6 31.0 1.0
CG D:ASN87 3.7 28.7 1.0
O D:ASP125 3.7 29.2 1.0
CB D:SER89 3.9 31.8 1.0
OG D:SER255 3.9 35.1 1.0
O D:HOH977 3.9 65.6 1.0
NZ D:LYS282 4.0 33.2 1.0
C D:ASP125 4.1 28.5 1.0
N D:SER89 4.1 29.8 1.0
CA D:LYS127 4.2 37.8 1.0
NH2 D:ARG85 4.2 30.8 1.0
N D:LYS127 4.3 34.7 1.0
ND2 D:ASN87 4.3 29.6 1.0
CB D:ASP125 4.3 26.2 1.0
OD2 D:ASP125 4.5 31.8 1.0
N D:THR126 4.5 29.1 1.0
CA D:SER89 4.6 30.6 1.0
O D:LYS127 4.6 41.4 1.0
CA D:THR126 4.6 30.3 1.0
N D:PHE88 4.6 27.2 1.0
C D:LYS127 4.7 40.9 1.0
O D:HOH769 4.8 40.6 1.0
CB D:ASN87 4.8 25.2 1.0
CA D:ASP125 4.8 26.1 1.0
CA D:ASN87 4.9 24.6 1.0
C D:ASN87 5.0 26.3 1.0

Potassium binding site 5 out of 8 in 7frw

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Potassium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:75.5
occ:1.00
 OD1 E:ASN87 2.6 55.8 1.0
OD1 E:ASP125 2.6 59.4 1.0
O E:THR126 2.7 60.0 1.0
OG E:SER89 2.8 66.2 1.0
O E:HOH870 3.1 57.7 1.0
C E:THR126 3.5 60.1 1.0
CG E:ASP125 3.6 58.9 1.0
O E:ASP125 3.6 54.8 1.0
CG E:ASN87 3.7 55.2 1.0
CB E:SER89 3.9 63.6 1.0
OG E:SER255 3.9 53.0 1.0
C E:ASP125 4.0 54.7 1.0
NZ E:LYS282 4.0 51.7 1.0
N E:SER89 4.1 60.7 1.0
CB E:ASP125 4.2 54.4 1.0
N E:LYS127 4.2 61.9 1.0
CA E:LYS127 4.2 63.8 1.0
NH2 E:ARG85 4.2 47.0 1.0
N E:THR126 4.4 55.9 1.0
ND2 E:ASN87 4.4 56.1 1.0
OD2 E:ASP125 4.4 61.0 1.0
N E:PHE88 4.5 56.0 1.0
CA E:THR126 4.5 57.7 1.0
CA E:SER89 4.5 62.1 1.0
O E:LYS127 4.6 65.7 1.0
CA E:ASP125 4.7 52.9 1.0
C E:LYS127 4.7 65.6 1.0
CA E:ASN87 4.8 52.2 1.0
CB E:ASN87 4.8 52.6 1.0
C E:ASN87 4.9 54.4 1.0
C E:PHE88 4.9 59.8 1.0

Potassium binding site 6 out of 8 in 7frw

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Potassium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:67.0
occ:1.00
 OD1 F:ASN87 2.6 43.3 1.0
OD1 F:ASP125 2.6 47.0 1.0
O F:THR126 2.7 43.9 1.0
OG F:SER89 2.9 51.8 1.0
O F:HOH729 3.0 59.2 1.0
O F:HOH828 3.0 55.9 1.0
CG F:ASP125 3.5 44.8 1.0
C F:THR126 3.6 44.5 1.0
O F:ASP125 3.6 38.9 1.0
CG F:ASN87 3.7 42.3 1.0
O F:HOH910 3.7 56.7 1.0
CB F:SER89 3.9 50.4 1.0
NZ F:LYS282 4.0 38.3 1.0
OG F:SER255 4.0 41.3 1.0
C F:ASP125 4.0 39.0 1.0
NH2 F:ARG85 4.1 41.1 1.0
CB F:ASP125 4.1 38.8 1.0
N F:SER89 4.1 48.3 1.0
N F:LYS127 4.3 46.4 1.0
CA F:LYS127 4.3 49.1 1.0
ND2 F:ASN87 4.3 43.3 1.0
OD2 F:ASP125 4.3 45.6 1.0
N F:THR126 4.4 40.5 1.0
N F:PHE88 4.6 42.2 1.0
CA F:THR126 4.6 42.4 1.0
CA F:SER89 4.6 50.0 1.0
CA F:ASP125 4.7 37.6 1.0
O F:LYS127 4.7 51.5 1.0
CA F:ASN87 4.7 38.6 1.0
CB F:ASN87 4.8 39.2 1.0
C F:LYS127 4.8 51.1 1.0
O F:HOH1026 4.8 70.4 1.0
C F:ASN87 4.9 40.6 1.0

Potassium binding site 7 out of 8 in 7frw

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Potassium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:49.3
occ:1.00
 OD1 G:ASP125 2.6 37.2 1.0
O G:THR126 2.7 31.6 1.0
OD1 G:ASN87 2.7 35.0 1.0
O G:HOH944 2.8 45.8 1.0
OG G:SER89 2.9 39.2 1.0
CG G:ASP125 3.6 34.8 1.0
C G:THR126 3.6 32.6 1.0
CG G:ASN87 3.8 34.4 1.0
O G:ASP125 3.8 28.8 1.0
OG G:SER255 3.8 35.4 1.0
NZ G:LYS282 3.9 33.8 1.0
CB G:SER89 4.0 37.0 1.0
O G:HOH1026 4.0 76.0 1.0
C G:ASP125 4.1 29.1 1.0
NH2 G:ARG85 4.2 37.9 1.0
N G:SER89 4.2 34.2 1.0
CA G:LYS127 4.2 36.2 1.0
CB G:ASP125 4.3 28.3 1.0
N G:LYS127 4.3 34.2 1.0
OD2 G:ASP125 4.4 36.4 1.0
ND2 G:ASN87 4.4 35.5 1.0
O G:HOH918 4.4 72.9 1.0
N G:THR126 4.4 29.8 1.0
O G:LYS127 4.6 37.6 1.0
O G:HOH934 4.6 119.7 1.0
CA G:THR126 4.6 30.9 1.0
CA G:SER89 4.6 36.1 1.0
C G:LYS127 4.7 37.8 1.0
N G:PHE88 4.7 30.1 1.0
O G:HOH780 4.7 42.6 1.0
CA G:ASP125 4.8 27.0 1.0
CB G:ASN87 4.9 30.6 1.0
CA G:ASN87 4.9 29.2 1.0

Potassium binding site 8 out of 8 in 7frw

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


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K605

b:44.0
occ:1.00
 OD1 H:ASN87 2.6 28.4 1.0
OD1 H:ASP125 2.6 32.2 1.0
O H:THR126 2.8 28.1 1.0
OG H:SER89 2.9 36.1 1.0
CG H:ASP125 3.6 30.8 1.0
C H:THR126 3.7 29.3 1.0
CG H:ASN87 3.7 27.6 1.0
O H:ASP125 3.7 25.7 1.0
NZ H:LYS282 3.9 31.0 1.0
OG H:SER255 3.9 30.6 1.0
CB H:SER89 3.9 33.5 1.0
C H:ASP125 4.1 25.9 1.0
N H:SER89 4.1 30.8 1.0
NH2 H:ARG85 4.2 29.5 1.0
CB H:ASP125 4.2 25.3 1.0
ND2 H:ASN87 4.3 27.2 1.0
CA H:LYS127 4.3 35.0 1.0
N H:LYS127 4.3 31.5 1.0
OD2 H:ASP125 4.4 34.0 1.0
N H:THR126 4.4 26.8 1.0
CA H:SER89 4.6 32.4 1.0
N H:PHE88 4.6 26.7 1.0
CA H:THR126 4.6 28.0 1.0
O H:LYS127 4.7 37.7 1.0
CB H:ASN87 4.8 25.0 1.0
CA H:ASP125 4.8 24.1 1.0
C H:LYS127 4.8 37.7 1.0
CA H:ASN87 4.8 24.5 1.0
C H:ASN87 4.9 25.8 1.0
O3 H:OXL603 5.0 43.6 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 18:55:51 2024

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