Atomistry » Magnesium » PDB 7f6e-7fs6 » 7fs3
Atomistry »
  Magnesium »
    PDB 7f6e-7fs6 »
      7fs3 »

Magnesium in PDB 7fs3: Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15, PDB code: 7fs3 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) 189.21 / 1.66
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.686, 113.23, 189.296, 90, 91.71, 90
R / Rfree (%) 19.6 / 21.3

Other elements in 7fs3:

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15 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 15 (pdb code 7fs3). 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 15, PDB code: 7fs3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7fs3

Go back to Magnesium Binding Sites List in 7fs3
Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:21.3
occ:1.00
 O2 A:OXL602 1.9 37.6 1.0
OD2 A:ASP308 2.0 39.6 1.0
OE2 A:GLU284 2.1 38.2 1.0
O A:HOH752 2.2 37.7 1.0
O1 A:OXL602 2.3 36.7 1.0
O A:HOH794 2.3 40.4 1.0
C2 A:OXL602 2.8 37.9 1.0
C1 A:OXL602 2.8 37.3 1.0
CG A:ASP308 3.1 37.7 1.0
CD A:GLU284 3.1 37.0 1.0
OE1 A:GLU284 3.5 37.4 1.0
CB A:ASP308 3.6 32.8 1.0
O4 A:OXL602 4.0 38.4 1.0
O3 A:OXL602 4.1 37.3 1.0
OD1 A:ASP308 4.2 38.6 1.0
NZ A:LYS282 4.2 33.0 1.0
N A:ASP308 4.3 30.5 1.0
O A:HOH964 4.4 56.6 1.0
CG A:GLU284 4.4 33.8 1.0
O A:HOH834 4.5 46.8 1.0
CE1 A:PHE256 4.6 40.4 1.0
CA A:ASP308 4.6 30.9 1.0
CE A:LYS282 4.6 32.7 1.0
CB A:ALA305 4.7 28.7 1.0
CB A:GLU284 4.9 31.2 1.0
CD1 A:PHE256 5.0 39.6 1.0

Magnesium binding site 2 out of 8 in 7fs3

Go back to Magnesium Binding Sites List in 7fs3
Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:17.7
occ:1.00
 O B:HOH727 2.0 34.2 1.0
OE2 B:GLU284 2.0 28.9 1.0
OD2 B:ASP308 2.1 32.5 1.0
O4 B:OXL602 2.2 31.8 1.0
O3 B:OXL602 2.2 31.1 1.0
O B:HOH763 2.3 30.5 1.0
C2 B:OXL602 2.9 32.1 1.0
C1 B:OXL602 2.9 31.4 1.0
CD B:GLU284 3.1 29.7 1.0
CG B:ASP308 3.1 31.2 1.0
OE1 B:GLU284 3.5 30.3 1.0
CB B:ASP308 3.6 26.8 1.0
O B:HOH886 4.0 56.5 1.0
O1 B:OXL602 4.1 31.2 1.0
NZ B:LYS282 4.2 32.4 1.0
O2 B:OXL602 4.2 32.6 1.0
OD1 B:ASP308 4.2 32.7 1.0
N B:ASP308 4.3 25.1 1.0
CG B:GLU284 4.4 28.6 1.0
CE1 B:PHE256 4.6 38.1 1.0
CA B:ASP308 4.6 25.5 1.0
CE B:LYS282 4.6 32.4 1.0
O B:HOH827 4.6 42.8 1.0
CB B:ALA305 4.6 24.0 1.0
CB B:GLU284 4.8 27.6 1.0
CD1 B:PHE256 4.9 37.1 1.0

Magnesium binding site 3 out of 8 in 7fs3

Go back to Magnesium Binding Sites List in 7fs3
Magnesium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:13.7
occ:1.00
 O C:HOH753 2.0 31.2 1.0
OE2 C:GLU284 2.0 24.8 1.0
O4 C:OXL602 2.1 30.1 1.0
OD2 C:ASP308 2.1 30.4 1.0
O3 C:OXL602 2.1 29.4 1.0
O C:HOH800 2.3 28.1 1.0
C1 C:OXL602 2.8 30.1 1.0
C2 C:OXL602 2.9 30.6 1.0
CD C:GLU284 3.1 25.5 1.0
CG C:ASP308 3.2 29.7 1.0
OE1 C:GLU284 3.5 24.3 1.0
CB C:ASP308 3.6 24.3 1.0
O2 C:OXL602 4.1 31.7 1.0
O C:HOH986 4.1 44.5 1.0
O1 C:OXL602 4.1 29.7 1.0
NZ C:LYS282 4.2 23.2 1.0
OD1 C:ASP308 4.3 31.4 1.0
N C:ASP308 4.3 24.0 1.0
CG C:GLU284 4.4 26.2 1.0
CE C:LYS282 4.5 21.9 1.0
O C:HOH887 4.6 36.8 1.0
CE1 C:PHE256 4.6 31.7 1.0
CA C:ASP308 4.6 23.7 1.0
CB C:ALA305 4.6 22.1 1.0
CB C:GLU284 4.8 24.5 1.0
CD1 C:PHE256 5.0 30.5 1.0

Magnesium binding site 4 out of 8 in 7fs3

Go back to Magnesium Binding Sites List in 7fs3
Magnesium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:11.9
occ:1.00
 OD2 D:ASP308 2.0 27.5 1.0
O1 D:OXL602 2.0 28.5 1.0
OE2 D:GLU284 2.1 26.5 1.0
O2 D:OXL602 2.2 24.3 1.0
O D:HOH844 2.2 29.0 1.0
O D:HOH747 2.3 23.5 1.0
C1 D:OXL602 2.8 27.7 1.0
C2 D:OXL602 2.9 25.6 1.0
CG D:ASP308 3.1 26.9 1.0
CD D:GLU284 3.1 24.2 1.0
OE1 D:GLU284 3.5 22.9 1.0
CB D:ASP308 3.6 22.6 1.0
O D:HOH965 4.1 47.9 1.0
O3 D:OXL602 4.1 28.3 1.0
O4 D:OXL602 4.1 24.9 1.0
OD1 D:ASP308 4.2 28.5 1.0
NZ D:LYS282 4.2 21.3 1.0
N D:ASP308 4.3 20.6 1.0
CG D:GLU284 4.4 23.8 1.0
CE1 D:PHE256 4.5 33.8 1.0
CA D:ASP308 4.6 20.9 1.0
CE D:LYS282 4.6 21.3 1.0
O D:HOH908 4.6 35.4 1.0
CB D:ALA305 4.6 20.7 1.0
CB D:GLU284 4.9 22.2 1.0
CD1 D:PHE256 5.0 32.7 1.0

Magnesium binding site 5 out of 8 in 7fs3

Go back to Magnesium Binding Sites List in 7fs3
Magnesium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:14.7
occ:1.00
 O3 E:OXL602 1.9 29.6 1.0
OD2 E:ASP308 1.9 28.1 1.0
OE2 E:GLU284 2.1 34.2 1.0
O E:HOH766 2.3 29.9 1.0
O E:HOH791 2.3 30.1 1.0
O4 E:OXL602 2.3 29.9 1.0
C1 E:OXL602 2.8 30.0 1.0
C2 E:OXL602 3.0 29.8 1.0
CG E:ASP308 3.0 29.0 1.0
CD E:GLU284 3.1 34.0 1.0
H5 E:O9I605 3.4 29.9 0.0
OE1 E:GLU284 3.5 32.7 1.0
CB E:ASP308 3.5 25.9 1.0
O1 E:OXL602 4.1 30.3 1.0
O E:HOH911 4.1 50.8 1.0
OD1 E:ASP308 4.1 30.6 1.0
O2 E:OXL602 4.2 30.0 1.0
NZ E:LYS282 4.3 33.6 1.0
C7 E:O9I605 4.3 29.9 1.0
O E:HOH925 4.3 36.1 1.0
N E:ASP308 4.3 25.1 1.0
CG E:GLU284 4.4 30.4 1.0
CE1 E:PHE256 4.5 40.1 1.0
H6 E:O9I605 4.5 30.3 0.0
O E:HOH801 4.5 35.7 1.0
O8 E:O9I605 4.5 29.8 1.0
CA E:ASP308 4.6 24.5 1.0
O E:HOH981 4.6 50.2 1.0
CE E:LYS282 4.7 32.6 1.0
CB E:ALA305 4.7 25.3 1.0
C8 E:O9I605 4.8 30.3 1.0
CB E:GLU284 4.9 28.9 1.0
H2 E:O9I605 4.9 30.7 0.0
CD1 E:PHE256 4.9 38.8 1.0

Magnesium binding site 6 out of 8 in 7fs3

Go back to Magnesium Binding Sites List in 7fs3
Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg603

b:16.3
occ:1.00
 OE2 F:GLU284 2.0 31.6 1.0
OD2 F:ASP308 2.0 33.3 1.0
O2 F:OXL602 2.1 33.5 1.0
O F:HOH748 2.1 34.6 1.0
O F:HOH752 2.2 31.6 1.0
O1 F:OXL602 2.2 31.9 1.0
C2 F:OXL602 2.9 33.2 1.0
C1 F:OXL602 3.0 32.2 1.0
CD F:GLU284 3.1 30.8 1.0
CG F:ASP308 3.1 30.1 1.0
OE1 F:GLU284 3.5 31.2 1.0
CB F:ASP308 3.6 25.7 1.0
O4 F:OXL602 4.1 33.7 1.0
O3 F:OXL602 4.1 31.6 1.0
NZ F:LYS282 4.2 30.2 1.0
OD1 F:ASP308 4.2 30.6 1.0
N F:ASP308 4.3 24.1 1.0
O F:HOH1001 4.3 53.4 1.0
CG F:GLU284 4.4 30.1 1.0
CA F:ASP308 4.6 24.3 1.0
CE1 F:PHE256 4.6 36.5 1.0
CE F:LYS282 4.6 29.8 1.0
O F:HOH796 4.6 41.3 1.0
CB F:ALA305 4.6 23.7 1.0
CB F:GLU284 4.9 27.4 1.0
CD1 F:PHE256 5.0 35.4 1.0

Magnesium binding site 7 out of 8 in 7fs3

Go back to Magnesium Binding Sites List in 7fs3
Magnesium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg4005

b:11.6
occ:1.00
 OE2 G:GLU284 2.0 23.1 1.0
OD2 G:ASP308 2.1 27.3 1.0
O1 G:OXL4004 2.1 26.6 1.0
O G:HOH4249 2.1 28.2 1.0
O2 G:OXL4004 2.2 29.0 1.0
O G:HOH4143 2.3 25.7 1.0
C1 G:OXL4004 2.9 27.4 1.0
C2 G:OXL4004 2.9 29.2 1.0
CD G:GLU284 3.1 23.3 1.0
CG G:ASP308 3.1 26.8 1.0
OE1 G:GLU284 3.4 24.3 1.0
CB G:ASP308 3.6 22.5 1.0
O G:HOH4339 4.0 41.0 1.0
O3 G:OXL4004 4.1 26.8 1.0
O G:HOH4436 4.2 44.8 1.0
NZ G:LYS282 4.2 22.0 1.0
OD1 G:ASP308 4.2 28.4 1.0
O4 G:OXL4004 4.3 30.5 1.0
N G:ASP308 4.3 22.5 1.0
CG G:GLU284 4.4 23.3 1.0
O G:HOH4294 4.5 37.7 1.0
CE1 G:PHE256 4.5 31.6 1.0
CE G:LYS282 4.6 20.9 1.0
CA G:ASP308 4.6 21.9 1.0
CB G:ALA305 4.6 18.9 1.0
CB G:GLU284 4.8 22.5 1.0
CD1 G:PHE256 4.9 30.3 1.0

Magnesium binding site 8 out of 8 in 7fs3

Go back to Magnesium Binding Sites List in 7fs3
Magnesium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 15


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 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg603

b:11.4
occ:1.00
 OE2 H:GLU284 2.0 25.2 1.0
OD2 H:ASP308 2.1 28.2 1.0
O3 H:OXL602 2.1 28.4 1.0
O4 H:OXL602 2.2 27.2 1.0
O H:HOH772 2.2 25.2 1.0
O H:HOH839 2.2 27.7 1.0
C2 H:OXL602 2.9 27.1 1.0
C1 H:OXL602 2.9 28.3 1.0
CD H:GLU284 3.1 23.4 1.0
CG H:ASP308 3.1 27.5 1.0
OE1 H:GLU284 3.5 23.5 1.0
CB H:ASP308 3.6 23.5 1.0
O H:HOH980 4.1 45.7 1.0
O1 H:OXL602 4.1 29.3 1.0
O2 H:OXL602 4.1 26.3 1.0
NZ H:LYS282 4.2 24.1 1.0
OD1 H:ASP308 4.2 29.1 1.0
N H:ASP308 4.3 21.1 1.0
CG H:GLU284 4.4 21.4 1.0
CE H:LYS282 4.5 23.4 1.0
CE1 H:PHE256 4.5 32.5 1.0
O H:HOH827 4.6 32.9 1.0
CA H:ASP308 4.6 21.6 1.0
CB H:ALA305 4.6 18.2 1.0
CB H:GLU284 4.8 21.2 1.0
CD1 H:PHE256 5.0 31.4 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 21:41:27 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy