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

Go back to Potassium Binding Sites List in 7qdn
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

Go back to Potassium Binding Sites List in 7qdn
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

Go back to Potassium Binding Sites List in 7qdn
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

Go back to Potassium Binding Sites List in 7qdn
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

Go back to Potassium Binding Sites List in 7qdn
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

Go back to Potassium Binding Sites List in 7qdn
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

Go back to Potassium Binding Sites List in 7qdn
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: Wed Apr 5 09:49:35 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy