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Magnesium 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
Potassium (K) 8 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 7qdn

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:48.5
occ:1.00
 O4 A:OXD602 2.0 50.0 1.0
O A:HOH750 2.1 45.3 1.0
OE2 A:GLU284 2.1 44.0 1.0
OD2 A:ASP308 2.1 48.9 1.0
O3 A:OXD602 2.1 48.7 1.0
O A:HOH724 2.3 40.4 1.0
C2 A:OXD602 2.7 49.8 1.0
C1 A:OXD602 2.7 49.0 1.0
CD A:GLU284 3.2 45.4 1.0
CG A:ASP308 3.2 47.8 1.0
OE1 A:GLU284 3.6 46.2 1.0
CB A:ASP308 3.7 42.6 1.0
O6 A:OXD602 3.9 50.3 1.0
O5 A:OXD602 4.0 48.5 1.0
NZ A:LYS282 4.2 43.3 1.0
O A:HOH883 4.3 49.7 1.0
OD1 A:ASP308 4.3 48.9 1.0
O A:HOH844 4.3 55.6 1.0
N A:ASP308 4.4 39.9 1.0
CE A:LYS282 4.4 44.2 1.0
CG A:GLU284 4.5 43.3 1.0
O A:HOH755 4.5 47.2 1.0
CA A:ASP308 4.7 40.9 1.0
CB A:ALA305 4.7 36.8 1.0

Magnesium binding site 2 out of 8 in 7qdn

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:42.8
occ:1.00
 OE2 B:GLU284 2.0 47.7 1.0
O6 B:OXD602 2.0 41.5 1.0
OD2 B:ASP308 2.1 43.1 1.0
O B:HOH816 2.1 40.0 1.0
O5 B:OXD602 2.2 39.8 1.0
O B:HOH758 2.3 42.4 1.0
C2 B:OXD602 2.8 41.4 1.0
C1 B:OXD602 2.9 40.5 1.0
CD B:GLU284 3.0 47.5 1.0
CG B:ASP308 3.2 41.4 1.0
OE1 B:GLU284 3.3 49.6 1.0
CB B:ASP308 3.7 37.0 1.0
O4 B:OXD602 4.1 41.2 1.0
NZ B:LYS282 4.1 41.0 1.0
O3 B:OXD602 4.1 40.3 1.0
O B:HOH887 4.2 49.4 1.0
OD1 B:ASP308 4.3 42.3 1.0
CG B:GLU284 4.3 42.9 1.0
N B:ASP308 4.4 34.8 1.0
O B:HOH792 4.4 42.3 1.0
CE B:LYS282 4.4 41.0 1.0
CB B:ALA305 4.6 34.1 1.0
CA B:ASP308 4.7 35.6 1.0
CE1 B:PHE256 4.7 49.9 1.0
CB B:GLU284 4.8 39.1 1.0
CD1 B:PHE256 4.9 49.0 1.0

Magnesium binding site 3 out of 8 in 7qdn

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:34.0
occ:1.00
 OE2 C:GLU284 2.0 34.6 1.0
O C:HOH718 2.1 38.0 1.0
O5 C:OXD602 2.1 35.8 1.0
OD2 C:ASP308 2.1 35.7 1.0
O C:HOH787 2.2 35.6 1.0
O6 C:OXD602 2.2 36.8 1.0
C1 C:OXD602 2.8 36.6 1.0
C2 C:OXD602 2.9 37.5 1.0
CD C:GLU284 3.1 33.6 1.0
CG C:ASP308 3.2 37.3 1.0
OE1 C:GLU284 3.5 33.3 1.0
CB C:ASP308 3.6 33.3 1.0
O C:HOH946 4.0 48.8 1.0
O3 C:OXD602 4.1 36.4 1.0
O4 C:OXD602 4.1 38.6 1.0
NZ C:LYS282 4.2 29.2 1.0
OD1 C:ASP308 4.3 39.0 1.0
N C:ASP308 4.3 32.1 1.0
CG C:GLU284 4.4 33.2 1.0
O C:HOH879 4.4 39.5 1.0
CE C:LYS282 4.5 28.1 1.0
CB C:ALA305 4.6 29.8 1.0
CA C:ASP308 4.6 32.5 1.0
CE1 C:PHE256 4.7 38.6 1.0
CB C:GLU284 4.8 31.6 1.0
CD1 C:PHE256 5.0 37.7 1.0

Magnesium binding site 4 out of 8 in 7qdn

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:30.3
occ:1.00
 OD2 D:ASP308 2.0 33.3 1.0
O D:HOH778 2.0 30.5 1.0
OE2 D:GLU284 2.0 29.9 1.0
O3 D:OXD602 2.1 33.0 1.0
O D:HOH820 2.1 34.3 1.0
O4 D:OXD602 2.2 31.6 1.0
C1 D:OXD602 2.9 33.4 1.0
C2 D:OXD602 2.9 32.3 1.0
CD D:GLU284 3.1 29.1 1.0
CG D:ASP308 3.1 33.5 1.0
OE1 D:GLU284 3.5 28.5 1.0
CB D:ASP308 3.6 28.9 1.0
O D:HOH962 4.0 40.5 1.0
O6 D:OXD602 4.1 32.4 1.0
NZ D:LYS282 4.1 30.2 1.0
O5 D:OXD602 4.2 33.9 1.0
OD1 D:ASP308 4.2 35.0 1.0
N D:ASP308 4.3 28.0 1.0
CG D:GLU284 4.4 29.8 1.0
O D:HOH770 4.5 33.3 1.0
CE D:LYS282 4.5 30.6 1.0
CA D:ASP308 4.6 27.8 1.0
O D:HOH1018 4.6 49.0 1.0
CE1 D:PHE256 4.6 43.6 1.0
CB D:ALA305 4.6 24.9 1.0
CB D:GLU284 4.8 29.1 1.0
O D:HOH709 4.8 51.6 1.0
CD1 D:PHE256 5.0 42.3 1.0

Magnesium binding site 5 out of 8 in 7qdn

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:47.8
occ:1.00
 OE2 E:GLU284 2.0 47.2 1.0
O5 E:OXD602 2.1 49.1 1.0
OD2 E:ASP308 2.1 44.4 1.0
O E:HOH800 2.1 44.3 1.0
O E:HOH740 2.2 45.5 1.0
O6 E:OXD602 2.3 48.5 1.0
C1 E:OXD602 2.9 49.2 1.0
C2 E:OXD602 3.0 49.1 1.0
CD E:GLU284 3.0 47.0 1.0
CG E:ASP308 3.2 43.8 1.0
OE1 E:GLU284 3.4 44.8 1.0
CB E:ASP308 3.7 40.2 1.0
NZ E:LYS282 4.1 45.1 1.0
O3 E:OXD602 4.1 49.4 1.0
O4 E:OXD602 4.2 49.4 1.0
OD1 E:ASP308 4.3 45.3 1.0
CG E:GLU284 4.3 44.5 1.0
O E:HOH803 4.4 46.5 1.0
CE E:LYS282 4.5 45.4 1.0
N E:ASP308 4.5 37.9 1.0
O E:HOH819 4.6 51.1 1.0
CB E:ALA305 4.6 37.0 1.0
CE1 E:PHE256 4.6 54.8 1.0
CA E:ASP308 4.7 39.0 1.0
CB E:GLU284 4.8 41.8 1.0
CD1 E:PHE256 4.9 53.7 1.0

Magnesium binding site 6 out of 8 in 7qdn

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:39.1
occ:1.00
 OE2 F:GLU284 2.0 37.6 1.0
O F:HOH733 2.0 38.0 1.0
OD2 F:ASP308 2.1 42.8 1.0
O F:HOH786 2.1 37.5 1.0
O4 F:OXD602 2.1 42.3 1.0
O3 F:OXD602 2.2 40.6 1.0
C1 F:OXD602 2.9 41.3 1.0
C2 F:OXD602 2.9 42.6 1.0
CD F:GLU284 3.0 38.7 1.0
CG F:ASP308 3.2 41.0 1.0
OE1 F:GLU284 3.4 39.9 1.0
CB F:ASP308 3.6 35.4 1.0
O F:HOH910 4.0 45.4 1.0
NZ F:LYS282 4.1 39.8 1.0
O5 F:OXD602 4.1 41.0 1.0
O6 F:OXD602 4.2 43.5 1.0
OD1 F:ASP308 4.3 41.5 1.0
O F:HOH758 4.3 42.4 1.0
CG F:GLU284 4.3 38.2 1.0
N F:ASP308 4.4 32.7 1.0
CE F:LYS282 4.4 38.4 1.0
CB F:ALA305 4.6 31.1 1.0
CA F:ASP308 4.7 33.5 1.0
CE1 F:PHE256 4.7 43.9 1.0
CB F:GLU284 4.8 35.3 1.0
CD1 F:PHE256 5.0 43.1 1.0

Magnesium binding site 7 out of 8 in 7qdn

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:31.6
occ:1.00
 OE2 G:GLU284 2.0 31.2 1.0
O3 G:OXD602 2.0 32.5 1.0
O G:HOH749 2.0 32.5 1.0
OD2 G:ASP308 2.1 34.9 1.0
O4 G:OXD602 2.1 34.5 1.0
O G:HOH862 2.1 35.4 1.0
C1 G:OXD602 2.8 33.7 1.0
C2 G:OXD602 2.8 34.8 1.0
CD G:GLU284 3.1 31.0 1.0
CG G:ASP308 3.2 36.1 1.0
OE1 G:GLU284 3.4 31.1 1.0
CB G:ASP308 3.6 31.8 1.0
O G:HOH942 3.9 41.9 1.0
O5 G:OXD602 4.0 33.6 1.0
O6 G:OXD602 4.1 36.0 1.0
NZ G:LYS282 4.2 30.1 1.0
OD1 G:ASP308 4.3 38.2 1.0
O G:HOH1023 4.3 47.6 1.0
N G:ASP308 4.3 30.7 1.0
CG G:GLU284 4.4 32.3 1.0
O G:HOH847 4.5 36.3 1.0
CE G:LYS282 4.6 30.7 1.0
CA G:ASP308 4.6 30.9 1.0
CB G:ALA305 4.7 29.1 1.0
CE1 G:PHE256 4.7 38.1 1.0
CB G:GLU284 4.8 31.3 1.0
CD1 G:PHE256 5.0 37.2 1.0

Magnesium binding site 8 out of 8 in 7qdn

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603

b:34.0
occ:1.00
 OD2 H:ASP308 2.0 35.6 1.0
OE2 H:GLU284 2.0 31.0 1.0
O5 H:OXD602 2.1 33.2 1.0
O H:HOH762 2.1 37.1 1.0
O H:HOH786 2.1 29.9 1.0
O6 H:OXD602 2.1 33.6 1.0
C2 H:OXD602 2.9 33.3 1.0
C1 H:OXD602 2.9 33.9 1.0
CG H:ASP308 3.1 34.9 1.0
CD H:GLU284 3.1 30.6 1.0
OE1 H:GLU284 3.5 30.7 1.0
CB H:ASP308 3.5 30.4 1.0
O H:HOH962 4.1 47.7 1.0
O H:HOH996 4.1 44.2 1.0
O3 H:OXD602 4.1 35.0 1.0
O4 H:OXD602 4.1 32.5 1.0
OD1 H:ASP308 4.2 35.1 1.0
NZ H:LYS282 4.2 32.4 1.0
N H:ASP308 4.3 29.4 1.0
O H:HOH924 4.3 38.3 1.0
O H:HOH1044 4.4 47.5 1.0
CG H:GLU284 4.4 30.2 1.0
CA H:ASP308 4.5 29.3 1.0
CE1 H:PHE256 4.5 39.8 1.0
CE H:LYS282 4.6 31.6 1.0
CB H:ALA305 4.6 28.0 1.0
CB H:GLU284 4.8 30.0 1.0
CD1 H:PHE256 4.9 38.8 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: Thu Apr 6 19:39:14 2023

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