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Potassium in PDB 7qdn: Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted

Enzymatic activity of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted

All present enzymatic activity of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted:
2.7.1.40;

Protein crystallography data

The structure of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted, PDB code: 7qdn was solved by A.Lulla, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 103.69 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 207.448, 112.687, 188.333, 90, 91.36, 90
R / Rfree (%) 20.5 / 21.7

Other elements in 7qdn:

The structure of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted also contains other interesting chemical elements:

Sodium (Na) 6 atoms
Magnesium (Mg) 8 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted (pdb code 7qdn). 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 Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted, PDB code: 7qdn:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 7qdn

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Potassium binding site 1 out of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:54.6
occ:1.00
 OD1 A:ASN87 2.5 50.0 1.0
OD1 A:ASP125 2.6 46.9 1.0
O A:THR126 2.7 51.9 1.0
OG A:SER89 2.7 61.4 1.0
O A:HOH755 2.9 47.2 1.0
O A:HOH883 3.2 49.7 1.0
C A:THR126 3.6 52.5 1.0
CG A:ASP125 3.6 47.5 1.0
CG A:ASN87 3.6 50.0 1.0
CB A:SER89 3.7 59.5 1.0
O A:ASP125 3.7 46.2 1.0
OG A:SER255 3.9 48.2 1.0
N A:SER89 4.0 56.8 1.0
C A:ASP125 4.1 46.3 1.0
NZ A:LYS282 4.1 43.3 1.0
CA A:LYS127 4.2 58.5 1.0
NH2 A:ARG85 4.2 48.0 1.0
N A:LYS127 4.2 55.1 1.0
CB A:ASP125 4.2 45.4 1.0
ND2 A:ASN87 4.3 50.7 1.0
CA A:SER89 4.4 58.5 1.0
O A:HOH902 4.4 48.7 1.0
N A:THR126 4.5 47.2 1.0
OD2 A:ASP125 4.5 48.7 1.0
N A:PHE88 4.6 51.1 1.0
CA A:THR126 4.6 49.4 1.0
O A:LYS127 4.6 59.8 1.0
CB A:ASN87 4.7 48.1 1.0
O A:HOH724 4.7 40.4 1.0
CA A:ASN87 4.7 47.7 1.0
C A:LYS127 4.8 59.8 1.0
CA A:ASP125 4.8 45.2 1.0
C A:ASN87 4.9 49.7 1.0
C A:PHE88 4.9 55.6 1.0

Potassium binding site 2 out of 8 in 7qdn

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Potassium binding site 2 out of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K604

b:52.3
occ:1.00
 OD1 B:ASP125 2.6 49.4 1.0
O B:HOH792 2.7 42.3 1.0
OD1 B:ASN87 2.7 46.3 1.0
O B:HOH887 2.8 49.4 1.0
O B:THR126 2.8 49.5 1.0
OG B:SER89 2.9 59.5 1.0
CG B:ASP125 3.5 49.0 1.0
OG B:SER255 3.6 43.9 1.0
NZ B:LYS282 3.8 41.0 1.0
CG B:ASN87 3.8 46.1 1.0
C B:THR126 3.8 49.8 1.0
CB B:SER89 3.9 57.5 1.0
O B:ASP125 4.0 43.2 1.0
NH2 B:ARG85 4.0 40.2 1.0
O B:HOH816 4.3 40.0 1.0
C B:ASP125 4.3 43.6 1.0
OD2 B:ASP125 4.3 51.5 1.0
ND2 B:ASN87 4.3 47.1 1.0
CB B:ASP125 4.3 44.0 1.0
O B:HOH901 4.3 47.0 1.0
CA B:LYS127 4.4 53.3 1.0
N B:SER89 4.4 54.3 1.0
N B:LYS127 4.5 51.1 1.0
O B:LYS127 4.6 53.5 1.0
N B:THR126 4.7 44.9 1.0
CA B:SER89 4.7 56.2 1.0
CB B:SER255 4.8 43.1 1.0
C B:LYS127 4.8 53.6 1.0
CA B:THR126 4.8 47.3 1.0
O6 B:OXD602 4.8 41.5 1.0
CB B:ASN87 4.9 44.1 1.0
O B:HOH758 4.9 42.4 1.0
CA B:ASP125 4.9 42.9 1.0
N B:PHE88 5.0 48.2 1.0

Potassium binding site 3 out of 8 in 7qdn

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Potassium binding site 3 out of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K604

b:39.8
occ:1.00
 OD1 C:ASN87 2.5 34.2 1.0
OD1 C:ASP125 2.6 35.7 1.0
O C:THR126 2.7 31.7 1.0
OG C:SER89 2.8 39.1 1.0
O C:HOH879 2.9 39.5 1.0
O C:HOH946 3.0 48.8 1.0
CG C:ASP125 3.6 35.5 1.0
C C:THR126 3.6 32.4 1.0
CG C:ASN87 3.7 33.7 1.0
CB C:SER89 3.7 37.0 1.0
OG C:SER255 3.7 32.0 1.0
O C:ASP125 3.8 29.7 1.0
N C:SER89 4.0 33.9 1.0
NZ C:LYS282 4.1 29.2 1.0
C C:ASP125 4.1 29.7 1.0
NH2 C:ARG85 4.2 35.0 1.0
ND2 C:ASN87 4.3 35.0 1.0
CA C:LYS127 4.3 36.4 1.0
CB C:ASP125 4.3 30.6 1.0
N C:LYS127 4.3 34.0 1.0
CA C:SER89 4.4 36.5 1.0
OD2 C:ASP125 4.4 37.5 1.0
N C:THR126 4.5 29.9 1.0
O C:HOH940 4.5 47.0 1.0
O C:LYS127 4.5 37.8 1.0
O C:HOH787 4.6 35.6 1.0
CA C:THR126 4.6 30.9 1.0
N C:PHE88 4.6 30.5 1.0
C C:LYS127 4.7 37.5 1.0
CB C:ASN87 4.8 31.6 1.0
CA C:ASN87 4.8 30.5 1.0
CA C:ASP125 4.8 29.2 1.0
CB C:SER255 4.9 29.5 1.0
C C:ASN87 4.9 30.8 1.0
C C:PHE88 5.0 33.3 1.0

Potassium binding site 4 out of 8 in 7qdn

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Potassium binding site 4 out of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K604

b:33.3
occ:1.00
 OD1 D:ASP125 2.6 29.3 1.0
O D:THR126 2.7 29.8 1.0
OD1 D:ASN87 2.7 26.9 1.0
OG D:SER89 2.8 31.6 1.0
O D:HOH962 2.9 40.5 1.0
O D:HOH770 3.0 33.3 1.0
C D:THR126 3.6 30.4 1.0
CG D:ASP125 3.6 29.3 1.0
OG D:SER255 3.7 31.6 1.0
CG D:ASN87 3.7 27.7 1.0
O D:ASP125 3.8 27.8 1.0
CB D:SER89 3.8 28.2 1.0
NZ D:LYS282 4.0 30.2 1.0
N D:SER89 4.1 26.9 1.0
C D:ASP125 4.1 27.4 1.0
CA D:LYS127 4.2 35.2 1.0
NH2 D:ARG85 4.2 28.8 1.0
N D:LYS127 4.3 32.3 1.0
ND2 D:ASN87 4.3 28.3 1.0
CB D:ASP125 4.4 25.6 1.0
O D:HOH984 4.5 48.9 1.0
N D:THR126 4.5 27.2 1.0
O D:LYS127 4.5 37.6 1.0
OD2 D:ASP125 4.5 30.4 1.0
CA D:SER89 4.5 27.5 1.0
O D:HOH778 4.6 30.5 1.0
CA D:THR126 4.6 28.5 1.0
C D:LYS127 4.7 37.2 1.0
O D:HOH999 4.7 45.2 1.0
N D:PHE88 4.7 25.9 1.0
CB D:SER255 4.8 31.0 1.0
CB D:ASN87 4.8 26.3 1.0
CA D:ASP125 4.9 26.2 1.0
CA D:ASN87 4.9 25.9 1.0

Potassium binding site 5 out of 8 in 7qdn

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Potassium binding site 5 out of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K604

b:62.3
occ:1.00
 OD1 E:ASP125 2.6 53.7 1.0
O E:THR126 2.6 52.4 1.0
OD1 E:ASN87 2.7 48.5 1.0
OG E:SER89 2.8 61.0 1.0
O E:HOH803 2.8 46.5 1.0
C E:THR126 3.6 53.0 1.0
CG E:ASP125 3.6 53.1 1.0
OG E:SER255 3.6 50.0 1.0
CG E:ASN87 3.8 47.9 1.0
CB E:SER89 3.8 58.5 1.0
O E:ASP125 3.8 48.2 1.0
NZ E:LYS282 4.0 45.1 1.0
C E:ASP125 4.1 48.1 1.0
N E:SER89 4.2 55.5 1.0
CA E:LYS127 4.2 58.5 1.0
N E:LYS127 4.2 55.4 1.0
NH2 E:ARG85 4.3 44.1 1.0
CB E:ASP125 4.3 48.6 1.0
ND2 E:ASN87 4.4 48.2 1.0
N E:THR126 4.5 48.9 1.0
OD2 E:ASP125 4.5 55.3 1.0
O E:LYS127 4.5 59.5 1.0
CA E:SER89 4.5 57.4 1.0
O E:HOH800 4.5 44.3 1.0
CA E:THR126 4.6 50.3 1.0
C E:LYS127 4.6 59.7 1.0
N E:PHE88 4.8 49.5 1.0
CB E:SER255 4.8 47.9 1.0
CA E:ASP125 4.8 47.0 1.0
CB E:ASN87 4.9 46.0 1.0
CA E:ASN87 4.9 45.9 1.0

Potassium binding site 6 out of 8 in 7qdn

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Potassium binding site 6 out of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K604

b:52.4
occ:1.00
 OD1 F:ASN87 2.6 42.8 1.0
OD1 F:ASP125 2.6 47.4 1.0
O F:THR126 2.6 47.3 1.0
OG F:SER89 2.7 49.5 1.0
O F:HOH910 3.0 45.4 1.0
O F:HOH758 3.0 42.4 1.0
CG F:ASP125 3.5 46.7 1.0
C F:THR126 3.6 47.5 1.0
CG F:ASN87 3.7 42.1 1.0
O F:ASP125 3.7 42.4 1.0
CB F:SER89 3.7 49.3 1.0
OG F:SER255 3.8 40.8 1.0
NZ F:LYS282 4.0 39.8 1.0
C F:ASP125 4.1 42.3 1.0
N F:SER89 4.1 48.0 1.0
NH2 F:ARG85 4.1 42.6 1.0
CB F:ASP125 4.2 41.9 1.0
CA F:LYS127 4.2 51.6 1.0
ND2 F:ASN87 4.3 43.4 1.0
N F:LYS127 4.3 49.1 1.0
O F:HOH922 4.3 46.2 1.0
OD2 F:ASP125 4.4 48.2 1.0
N F:THR126 4.5 43.5 1.0
CA F:SER89 4.5 49.4 1.0
O F:LYS127 4.6 51.8 1.0
CA F:THR126 4.6 45.3 1.0
N F:PHE88 4.7 42.6 1.0
C F:LYS127 4.8 51.8 1.0
CB F:ASN87 4.8 39.5 1.0
CA F:ASP125 4.8 40.6 1.0
O F:HOH733 4.8 38.0 1.0
CA F:ASN87 4.8 39.5 1.0
C F:ASN87 5.0 40.9 1.0
CB F:SER255 5.0 39.0 1.0

Potassium binding site 7 out of 8 in 7qdn

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Potassium binding site 7 out of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K604

b:40.2
occ:1.00
 OD1 G:ASN87 2.6 31.1 1.0
OD1 G:ASP125 2.6 32.6 1.0
OG G:SER89 2.7 38.8 1.0
O G:THR126 2.7 30.6 1.0
O G:HOH847 2.8 36.3 1.0
O G:HOH942 2.9 41.9 1.0
CG G:ASP125 3.7 32.1 1.0
C G:THR126 3.7 30.7 1.0
OG G:SER255 3.7 28.9 1.0
CG G:ASN87 3.7 31.6 1.0
CB G:SER89 3.7 36.9 1.0
O G:ASP125 3.9 28.9 1.0
NZ G:LYS282 4.0 30.1 1.0
N G:SER89 4.1 33.1 1.0
C G:ASP125 4.2 28.7 1.0
NH2 G:ARG85 4.2 32.1 1.0
CA G:LYS127 4.2 34.0 1.0
ND2 G:ASN87 4.3 32.6 1.0
N G:LYS127 4.3 31.9 1.0
O G:HOH928 4.3 43.0 1.0
CB G:ASP125 4.4 27.5 1.0
OD2 G:ASP125 4.5 34.3 1.0
O G:LYS127 4.5 35.2 1.0
CA G:SER89 4.5 36.0 1.0
N G:THR126 4.5 28.9 1.0
O G:HOH961 4.5 44.8 1.0
O G:HOH749 4.6 32.5 1.0
C G:LYS127 4.7 35.2 1.0
CA G:THR126 4.7 29.9 1.0
N G:PHE88 4.8 27.9 1.0
CB G:SER255 4.9 27.6 1.0
CB G:ASN87 4.9 28.8 1.0
CA G:ASP125 4.9 26.9 1.0
CA G:ASN87 4.9 27.4 1.0

Potassium binding site 8 out of 8 in 7qdn

Go back to Potassium Binding Sites List in 7qdn
Potassium binding site 8 out of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K604

b:36.8
occ:1.00
 OD1 H:ASP125 2.6 31.4 1.0
OD1 H:ASN87 2.6 30.1 1.0
O H:THR126 2.8 29.1 1.0
OG H:SER89 2.8 34.9 1.0
O H:HOH996 2.8 44.2 1.0
O H:HOH924 2.9 38.3 1.0
CG H:ASP125 3.6 30.5 1.0
CG H:ASN87 3.7 29.1 1.0
C H:THR126 3.7 30.5 1.0
CB H:SER89 3.8 33.1 1.0
OG H:SER255 3.8 31.8 1.0
O H:ASP125 3.9 27.2 1.0
NZ H:LYS282 4.0 32.4 1.0
N H:SER89 4.1 31.2 1.0
C H:ASP125 4.2 27.1 1.0
NH2 H:ARG85 4.2 32.4 1.0
ND2 H:ASN87 4.2 29.4 1.0
O H:HOH1022 4.3 44.9 1.0
CA H:LYS127 4.3 37.0 1.0
O H:HOH976 4.4 50.0 1.0
N H:LYS127 4.4 33.0 1.0
CB H:ASP125 4.4 26.4 1.0
OD2 H:ASP125 4.4 31.7 1.0
CA H:SER89 4.5 32.6 1.0
N H:THR126 4.5 27.6 1.0
O H:HOH786 4.6 29.9 1.0
O H:LYS127 4.6 38.7 1.0
N H:PHE88 4.7 28.4 1.0
CA H:THR126 4.7 28.9 1.0
C H:LYS127 4.8 38.6 1.0
CB H:ASN87 4.8 27.1 1.0
CA H:ASN87 4.9 27.0 1.0
CA H:ASP125 4.9 25.8 1.0
CB H:SER255 4.9 29.9 1.0
C H:ASN87 5.0 27.8 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: Mon Aug 12 20:27:49 2024

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