Atomistry » Magnesium » PDB 5scg-5seq » 5scl
Atomistry »
  Magnesium »
    PDB 5scg-5seq »
      5scl »

Magnesium in PDB 5scl: Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1, PDB code: 5scl was solved by A.Lulla, A.Foller, A.Nain-Perez, M.Grotli, P.Brear, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 187.75 / 2.13
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 206.875, 112.269, 187.907, 90, 92.32, 90
R / Rfree (%) 19.8 / 22.2

Other elements in 5scl:

The structure of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1 also contains other interesting chemical elements:

Potassium (K) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1 (pdb code 5scl). 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 Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1, PDB code: 5scl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5scl

Go back to Magnesium Binding Sites List in 5scl
Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:65.0
occ:1.00
 OD2 A:ASP308 2.1 60.9 1.0
OE2 A:GLU284 2.2 64.4 1.0
O2 A:OXL602 2.3 60.8 1.0
O1 A:OXL602 2.5 59.6 1.0
CD A:GLU284 3.1 61.6 1.0
C2 A:OXL602 3.2 60.6 1.0
C1 A:OXL602 3.3 59.5 1.0
CG A:ASP308 3.3 58.8 1.0
OE1 A:GLU284 3.4 61.0 1.0
CB A:ASP308 4.0 52.5 1.0
NZ A:LYS282 4.1 57.8 1.0
OD1 A:ASP308 4.3 60.2 1.0
O4 A:OXL602 4.4 61.1 1.0
O3 A:OXL602 4.5 58.7 1.0
CG A:GLU284 4.5 55.6 1.0
CE A:LYS282 4.5 56.3 1.0
CE1 A:PHE256 4.8 54.9 1.0
N A:ASP308 4.8 49.0 1.0
CD1 A:PHE256 4.9 54.0 1.0

Magnesium binding site 2 out of 8 in 5scl

Go back to Magnesium Binding Sites List in 5scl
Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:50.4
occ:1.00
 O4 B:OXL602 1.9 54.9 1.0
OE2 B:GLU284 2.0 43.0 1.0
OD2 B:ASP308 2.1 55.5 1.0
O B:HOH773 2.3 45.5 1.0
O3 B:OXL602 2.5 52.1 1.0
C2 B:OXL602 2.9 54.2 1.0
CD B:GLU284 3.0 44.2 1.0
C1 B:OXL602 3.1 52.7 1.0
CG B:ASP308 3.2 53.6 1.0
OE1 B:GLU284 3.3 47.4 1.0
CB B:ASP308 3.8 48.1 1.0
O2 B:OXL602 4.1 54.6 1.0
NZ B:LYS282 4.1 45.7 1.0
O1 B:OXL602 4.3 51.7 1.0
OD1 B:ASP308 4.3 54.5 1.0
CG B:GLU284 4.3 44.0 1.0
CE B:LYS282 4.5 43.7 1.0
N B:ASP308 4.6 43.8 1.0
CE1 B:PHE256 4.7 47.6 1.0
CB B:ALA305 4.8 39.1 1.0
CB B:GLU284 4.8 43.5 1.0
CA B:ASP308 4.8 45.0 1.0
CD1 B:PHE256 4.9 46.8 1.0
O B:HOH865 4.9 59.3 1.0

Magnesium binding site 3 out of 8 in 5scl

Go back to Magnesium Binding Sites List in 5scl
Magnesium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:57.6
occ:1.00
 OD2 C:ASP308 2.1 52.1 1.0
OE2 C:GLU284 2.2 44.7 1.0
O4 C:OXL602 2.3 61.6 1.0
O3 C:OXL602 2.3 60.9 1.0
C1 C:OXL602 3.1 60.8 1.0
C2 C:OXL602 3.1 61.5 1.0
CD C:GLU284 3.1 43.6 1.0
CG C:ASP308 3.2 51.0 1.0
OE1 C:GLU284 3.4 45.7 1.0
O C:HOH838 3.7 52.5 1.0
CB C:ASP308 3.8 44.6 1.0
NZ C:LYS282 4.1 42.6 1.0
OD1 C:ASP308 4.3 53.6 1.0
O2 C:OXL602 4.3 62.1 1.0
O1 C:OXL602 4.4 60.0 1.0
CG C:GLU284 4.5 42.3 1.0
CE C:LYS282 4.6 41.0 1.0
N C:ASP308 4.7 40.8 1.0
CE1 C:PHE256 4.8 41.4 1.0
CA C:ASP308 4.9 42.2 1.0
CB C:ALA305 4.9 37.0 1.0
CB C:GLU284 5.0 41.7 1.0
CD1 C:PHE256 5.0 40.9 1.0

Magnesium binding site 4 out of 8 in 5scl

Go back to Magnesium Binding Sites List in 5scl
Magnesium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:49.0
occ:1.00
 OD2 D:ASP308 1.9 45.1 1.0
O D:HOH757 2.2 39.2 1.0
O1 D:OXL602 2.2 45.3 1.0
OE2 D:GLU284 2.3 45.3 1.0
O2 D:OXL602 2.3 42.4 1.0
C1 D:OXL602 3.0 44.0 1.0
C2 D:OXL602 3.1 43.2 1.0
CG D:ASP308 3.1 44.3 1.0
CD D:GLU284 3.3 41.4 1.0
OE1 D:GLU284 3.7 40.7 1.0
CB D:ASP308 3.8 38.9 1.0
OD1 D:ASP308 4.1 45.6 1.0
O4 D:OXL602 4.2 43.1 1.0
NZ D:LYS282 4.3 32.6 1.0
O3 D:OXL602 4.3 43.2 1.0
N D:ASP308 4.5 36.4 1.0
O D:HOH828 4.6 67.5 1.0
CG D:GLU284 4.7 36.6 1.0
CA D:ASP308 4.7 37.0 1.0
CE D:LYS282 4.8 30.3 1.0
CB D:ALA305 4.9 28.8 1.0
CE1 D:PHE256 4.9 39.5 1.0

Magnesium binding site 5 out of 8 in 5scl

Go back to Magnesium Binding Sites List in 5scl
Magnesium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg604

b:56.6
occ:1.00
 OE2 E:GLU284 1.9 60.1 1.0
OD2 E:ASP308 2.2 60.1 1.0
O3 E:OXL602 2.3 64.5 1.0
O4 E:OXL602 2.3 62.8 1.0
O E:HOH755 2.4 54.1 1.0
CD E:GLU284 2.9 57.2 1.0
C1 E:OXL602 3.1 64.1 1.0
C2 E:OXL602 3.1 63.4 1.0
OE1 E:GLU284 3.2 57.0 1.0
CG E:ASP308 3.3 58.6 1.0
CB E:ASP308 3.8 50.9 1.0
NZ E:LYS282 3.9 49.4 1.0
CG E:GLU284 4.3 53.3 1.0
O2 E:OXL602 4.3 63.4 1.0
CE E:LYS282 4.3 49.0 1.0
O1 E:OXL602 4.4 63.8 1.0
OD1 E:ASP308 4.4 61.2 1.0
O E:HOH836 4.6 50.8 1.0
CB E:ALA305 4.6 47.3 1.0
N E:ASP308 4.6 47.4 1.0
CB E:GLU284 4.7 51.0 1.0
CE1 E:PHE256 4.8 54.3 1.0
CA E:ASP308 4.9 48.3 1.0
CD1 E:PHE256 4.9 53.7 1.0

Magnesium binding site 6 out of 8 in 5scl

Go back to Magnesium Binding Sites List in 5scl
Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg604

b:45.9
occ:1.00
 OE2 F:GLU284 2.0 42.0 1.0
OD2 F:ASP308 2.0 49.9 1.0
O F:HOH728 2.1 37.9 1.0
O1 F:OXL602 2.2 61.9 1.0
O F:HOH750 2.3 56.4 1.0
O2 F:OXL602 2.3 63.3 1.0
CD F:GLU284 3.0 45.0 1.0
C1 F:OXL602 3.1 62.1 1.0
C2 F:OXL602 3.1 63.1 1.0
CG F:ASP308 3.1 49.5 1.0
OE1 F:GLU284 3.4 47.2 1.0
CB F:ASP308 3.6 43.9 1.0
NZ F:LYS282 4.2 47.6 1.0
OD1 F:ASP308 4.2 51.3 1.0
O3 F:OXL602 4.2 61.4 1.0
O4 F:OXL602 4.3 63.6 1.0
CG F:GLU284 4.3 42.4 1.0
O F:HOH814 4.4 52.0 1.0
N F:ASP308 4.5 39.3 1.0
CE F:LYS282 4.6 45.2 1.0
CA F:ASP308 4.7 40.9 1.0
CB F:ALA305 4.7 37.4 1.0
CE1 F:PHE256 4.7 46.1 1.0
CB F:GLU284 4.8 39.5 1.0
CD1 F:PHE256 4.9 45.4 1.0

Magnesium binding site 7 out of 8 in 5scl

Go back to Magnesium Binding Sites List in 5scl
Magnesium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg604

b:39.3
occ:1.00
 O G:HOH766 1.9 31.9 1.0
OD2 G:ASP308 2.0 49.7 1.0
OE2 G:GLU284 2.2 44.9 1.0
O2 G:OXL602 2.2 45.7 1.0
O G:HOH714 2.3 42.3 1.0
O1 G:OXL602 2.3 45.2 1.0
C2 G:OXL602 3.0 45.2 1.0
C1 G:OXL602 3.1 45.2 1.0
CD G:GLU284 3.2 41.8 1.0
CG G:ASP308 3.2 46.8 1.0
OE1 G:GLU284 3.5 42.1 1.0
CB G:ASP308 3.8 42.5 1.0
O G:HOH924 4.0 64.6 1.0
O G:HOH780 4.1 41.8 1.0
NZ G:LYS282 4.2 38.1 1.0
OD1 G:ASP308 4.2 45.9 1.0
O3 G:OXL602 4.3 45.4 1.0
O4 G:OXL602 4.3 44.2 1.0
CG G:GLU284 4.5 39.4 1.0
O G:HOH825 4.6 57.6 1.0
N G:ASP308 4.6 39.7 1.0
CE G:LYS282 4.6 36.4 1.0
CE1 G:PHE256 4.8 39.8 1.0
CA G:ASP308 4.8 40.9 1.0
CB G:ALA305 4.9 36.8 1.0
CD1 G:PHE256 5.0 39.0 1.0
CB G:GLU284 5.0 37.5 1.0

Magnesium binding site 8 out of 8 in 5scl

Go back to Magnesium Binding Sites List in 5scl
Magnesium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Liver Pyruvate Kinase in Complex with Anthraquinone Derivative 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:45.0
occ:1.00
 OD2 H:ASP308 2.0 42.4 1.0
O4 H:OXL602 2.1 39.9 1.0
O3 H:OXL602 2.2 43.6 1.0
OE2 H:GLU284 2.2 42.7 1.0
O H:HOH743 2.3 39.1 1.0
C2 H:OXL602 2.9 41.2 1.0
C1 H:OXL602 2.9 42.9 1.0
CG H:ASP308 3.1 39.9 1.0
CD H:GLU284 3.3 40.1 1.0
CB H:ASP308 3.7 37.0 1.0
OE1 H:GLU284 3.7 38.8 1.0
O2 H:OXL602 4.1 41.4 1.0
O H:HOH885 4.1 49.7 1.0
OD1 H:ASP308 4.2 40.0 1.0
O1 H:OXL602 4.2 43.3 1.0
NZ H:LYS282 4.3 32.0 1.0
N H:ASP308 4.3 35.7 1.0
CA H:ASP308 4.6 36.3 1.0
CG H:GLU284 4.6 36.4 1.0
CE H:LYS282 4.7 29.9 1.0
CB H:ALA305 4.8 34.6 1.0
CB H:GLU284 5.0 35.0 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 11:04:05 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