Atomistry » Magnesium » PDB 7f6e-7fs6 » 7fs0
Atomistry »
  Magnesium »
    PDB 7f6e-7fs6 »
      7fs0 »

Magnesium in PDB 7fs0: Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8, PDB code: 7fs0 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) 189.45 / 2.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.002, 113.344, 189.484, 90, 91.12, 90
R / Rfree (%) 21.9 / 25.3

Other elements in 7fs0:

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8 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 Allosteric Modulator 8 (pdb code 7fs0). 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 Allosteric Modulator 8, PDB code: 7fs0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7fs0

Go back to Magnesium Binding Sites List in 7fs0
Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


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 Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:62.0
occ:1.00
 O1 A:OXL602 2.0 144.1 1.0
OD2 A:ASP308 2.0 92.1 1.0
OE2 A:GLU284 2.1 96.2 1.0
O2 A:OXL602 2.1 144.2 1.0
C1 A:OXL602 2.7 144.1 1.0
C2 A:OXL602 2.8 144.1 1.0
CD A:GLU284 3.2 93.8 1.0
CG A:ASP308 3.2 90.4 1.0
OE1 A:GLU284 3.6 95.4 1.0
CB A:ASP308 3.9 86.3 1.0
O3 A:OXL602 3.9 144.1 1.0
O4 A:OXL602 4.0 144.0 1.0
OD1 A:ASP308 4.2 91.2 1.0
NZ A:LYS282 4.3 87.2 1.0
CG A:GLU284 4.5 87.0 1.0
N A:ASP308 4.5 84.2 1.0
CE A:LYS282 4.7 84.7 1.0
CB A:ALA305 4.8 80.4 1.0
CA A:ASP308 4.8 84.9 1.0
CE1 A:PHE256 4.9 95.9 1.0
CB A:GLU284 5.0 81.9 1.0
O A:HOH740 5.0 63.8 1.0

Magnesium binding site 2 out of 8 in 7fs0

Go back to Magnesium Binding Sites List in 7fs0
Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


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 Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:59.8
occ:1.00
 O4 B:OXL602 2.0 80.0 1.0
OD2 B:ASP308 2.0 70.0 1.0
OE2 B:GLU284 2.1 84.7 1.0
O3 B:OXL602 2.1 77.3 1.0
C2 B:OXL602 2.7 79.3 1.0
C1 B:OXL602 2.8 78.0 1.0
CG B:ASP308 3.2 69.6 1.0
CD B:GLU284 3.2 84.0 1.0
OE1 B:GLU284 3.6 87.6 1.0
CB B:ASP308 3.8 63.3 1.0
O1 B:OXL602 4.0 77.7 1.0
O2 B:OXL602 4.0 79.2 1.0
OD1 B:ASP308 4.2 72.1 1.0
NZ B:LYS282 4.3 82.7 1.0
N B:ASP308 4.4 58.2 1.0
CG B:GLU284 4.5 76.2 1.0
CE B:LYS282 4.7 80.3 1.0
CA B:ASP308 4.8 59.8 1.0
CB B:ALA305 4.8 55.5 1.0
CE1 B:PHE256 4.9 83.8 1.0
CB B:GLU284 5.0 71.0 1.0

Magnesium binding site 3 out of 8 in 7fs0

Go back to Magnesium Binding Sites List in 7fs0
Magnesium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


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 Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:56.5
occ:1.00
 OE2 C:GLU284 1.9 54.2 1.0
OD2 C:ASP308 2.0 79.6 1.0
O3 C:OXL602 2.1 78.2 1.0
O4 C:OXL602 2.1 78.9 1.0
O C:HOH719 2.4 55.9 1.0
C1 C:OXL602 2.9 78.2 1.0
CD C:GLU284 2.9 58.5 1.0
C2 C:OXL602 2.9 78.5 1.0
CG C:ASP308 3.2 77.7 1.0
OE1 C:GLU284 3.3 63.1 1.0
CB C:ASP308 3.9 71.5 1.0
O2 C:OXL602 4.1 78.3 1.0
O1 C:OXL602 4.2 78.0 1.0
NZ C:LYS282 4.2 61.0 1.0
OD1 C:ASP308 4.2 79.2 1.0
CG C:GLU284 4.3 56.5 1.0
CE C:LYS282 4.6 58.1 1.0
CE1 C:PHE256 4.7 57.2 1.0
N C:ASP308 4.7 67.9 1.0
CB C:GLU284 4.8 55.1 1.0
CB C:ALA305 4.9 60.8 1.0
CD1 C:PHE256 4.9 56.4 1.0
CA C:ASP308 4.9 69.3 1.0

Magnesium binding site 4 out of 8 in 7fs0

Go back to Magnesium Binding Sites List in 7fs0
Magnesium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


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 Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:36.5
occ:1.00
 OD2 D:ASP308 1.9 58.3 1.0
O2 D:OXL602 2.0 62.6 1.0
OE2 D:GLU284 2.2 58.1 1.0
O1 D:OXL602 2.5 64.8 1.0
C2 D:OXL602 2.9 63.0 1.0
CG D:ASP308 3.1 56.6 1.0
C1 D:OXL602 3.2 63.9 1.0
CD D:GLU284 3.3 57.2 1.0
OE1 D:GLU284 3.7 58.1 1.0
CB D:ASP308 3.9 51.9 1.0
OD1 D:ASP308 4.1 57.4 1.0
O4 D:OXL602 4.1 62.4 1.0
NZ D:LYS282 4.3 44.9 1.0
O3 D:OXL602 4.4 63.6 1.0
N D:ASP308 4.6 48.9 1.0
CG D:GLU284 4.6 54.2 1.0
CE D:LYS282 4.8 41.6 1.0
CA D:ASP308 4.8 49.9 1.0
CE1 D:PHE256 4.9 54.4 1.0
CB D:ALA305 5.0 41.2 1.0

Magnesium binding site 5 out of 8 in 7fs0

Go back to Magnesium Binding Sites List in 7fs0
Magnesium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


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 Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:46.8
occ:1.00
 OE2 E:GLU284 1.9 75.2 1.0
OD2 E:ASP308 1.9 83.3 1.0
O4 E:OXL602 2.0 89.2 1.0
O3 E:OXL602 2.2 89.8 1.0
C2 E:OXL602 2.7 89.4 1.0
C1 E:OXL602 2.8 89.9 1.0
CD E:GLU284 3.0 75.5 1.0
CG E:ASP308 3.1 79.9 1.0
OE1 E:GLU284 3.5 76.8 1.0
CB E:ASP308 3.7 73.2 1.0
O2 E:OXL602 3.9 89.4 1.0
O1 E:OXL602 4.1 90.0 1.0
OD1 E:ASP308 4.1 80.8 1.0
NZ E:LYS282 4.3 71.7 1.0
CG E:GLU284 4.3 72.2 1.0
N E:ASP308 4.4 69.6 1.0
CA E:ASP308 4.7 70.4 1.0
CE E:LYS282 4.7 70.9 1.0
CB E:ALA305 4.7 65.3 1.0
CB E:GLU284 4.8 69.5 1.0
CE1 E:PHE256 4.8 78.3 1.0

Magnesium binding site 6 out of 8 in 7fs0

Go back to Magnesium Binding Sites List in 7fs0
Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


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 Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg603

b:38.4
occ:1.00
 OD2 F:ASP308 2.0 58.5 1.0
O1 F:OXL602 2.2 90.0 1.0
OE2 F:GLU284 2.2 52.1 1.0
O2 F:OXL602 2.3 91.2 1.0
C1 F:OXL602 3.0 90.3 1.0
C2 F:OXL602 3.1 90.8 1.0
CG F:ASP308 3.2 57.0 1.0
CD F:GLU284 3.3 54.0 1.0
OE1 F:GLU284 3.6 57.7 1.0
CB F:ASP308 3.9 49.8 1.0
OD1 F:ASP308 4.1 60.1 1.0
O3 F:OXL602 4.2 90.1 1.0
NZ F:LYS282 4.3 51.7 1.0
O4 F:OXL602 4.3 90.8 1.0
CG F:GLU284 4.6 48.9 1.0
N F:ASP308 4.6 44.9 1.0
CE F:LYS282 4.7 49.3 1.0
CA F:ASP308 4.9 47.1 1.0
CE1 F:PHE256 4.9 59.6 1.0
CB F:ALA305 4.9 41.9 1.0

Magnesium binding site 7 out of 8 in 7fs0

Go back to Magnesium Binding Sites List in 7fs0
Magnesium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


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 Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:31.3
occ:1.00
 O1 G:OXL602 1.9 56.0 1.0
OE2 G:GLU284 2.0 49.1 1.0
OD2 G:ASP308 2.1 64.1 1.0
O2 G:OXL602 2.4 58.2 1.0
C1 G:OXL602 2.8 56.4 1.0
C2 G:OXL602 3.0 57.6 1.0
CD G:GLU284 3.0 50.8 1.0
OE1 G:GLU284 3.3 53.7 1.0
CG G:ASP308 3.3 61.8 1.0
O G:HOH759 3.8 63.7 1.0
O3 G:OXL602 4.0 55.7 1.0
NZ G:LYS282 4.0 40.5 1.0
CB G:ASP308 4.0 55.3 1.0
O4 G:OXL602 4.3 58.0 1.0
OD1 G:ASP308 4.3 63.2 1.0
CG G:GLU284 4.4 47.3 1.0
CE G:LYS282 4.5 39.9 1.0
CE1 G:PHE256 4.8 48.8 1.0
N G:ASP308 4.8 51.5 1.0
CB G:ALA305 4.9 48.5 1.0
CB G:GLU284 5.0 44.1 1.0
CD1 G:PHE256 5.0 48.0 1.0

Magnesium binding site 8 out of 8 in 7fs0

Go back to Magnesium Binding Sites List in 7fs0
Magnesium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 8


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 Allosteric Modulator 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:28.8
occ:1.00
 O4 H:OXL602 1.9 54.3 1.0
OE2 H:GLU284 1.9 54.9 1.0
OD2 H:ASP308 2.0 54.8 1.0
O3 H:OXL602 2.6 56.5 1.0
O H:HOH851 2.8 47.2 1.0
C2 H:OXL602 2.9 55.4 1.0
CD H:GLU284 3.0 52.5 1.0
CG H:ASP308 3.2 52.1 1.0
C1 H:OXL602 3.2 56.2 1.0
OE1 H:GLU284 3.3 56.1 1.0
CB H:ASP308 3.9 46.1 1.0
O2 H:OXL602 4.1 55.8 1.0
NZ H:LYS282 4.1 42.1 1.0
OD1 H:ASP308 4.2 52.9 1.0
CG H:GLU284 4.3 45.3 1.0
O1 H:OXL602 4.4 56.5 1.0
CE H:LYS282 4.5 39.8 1.0
O H:HOH928 4.7 46.9 1.0
CE1 H:PHE256 4.7 47.2 1.0
O H:HOH901 4.7 55.5 1.0
N H:ASP308 4.7 42.3 1.0
CB H:GLU284 4.8 42.0 1.0
CB H:ALA305 4.9 33.8 1.0
CD1 H:PHE256 4.9 46.4 1.0
CA H:ASP308 4.9 43.9 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: Wed Oct 2 21:38:01 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy