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Magnesium in PDB 7frw: Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4, PDB code: 7frw 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) 104.04 / 1.74
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.144, 112.752, 188.438, 90, 91.41, 90
R / Rfree (%) 20.2 / 22

Other elements in 7frw:

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

Magnesium binding site 1 out of 8 in 7frw

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Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:74.9
occ:1.00
 O2 A:OXL602 2.2 75.2 1.0
OD2 A:ASP308 2.2 57.8 1.0
OE2 A:GLU284 2.2 59.8 1.0
O1 A:OXL602 2.3 74.6 1.0
C2 A:OXL602 2.9 75.2 1.0
C1 A:OXL602 2.9 74.8 1.0
CD A:GLU284 3.1 58.2 1.0
CG A:ASP308 3.3 55.1 1.0
OE1 A:GLU284 3.4 59.3 1.0
CB A:ASP308 3.9 49.6 1.0
NZ A:LYS282 4.1 54.8 1.0
O4 A:OXL602 4.1 75.4 1.0
O3 A:OXL602 4.2 74.7 1.0
OD1 A:ASP308 4.4 55.7 1.0
CE A:LYS282 4.5 53.2 1.0
CG A:GLU284 4.5 52.0 1.0
N A:ASP308 4.7 46.3 1.0
CE1 A:PHE256 4.8 57.5 1.0
CB A:ALA305 4.8 43.9 1.0
CA A:ASP308 4.9 47.5 1.0
CD1 A:PHE256 5.0 56.7 1.0
CB A:GLU284 5.0 47.0 1.0

Magnesium binding site 2 out of 8 in 7frw

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Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:60.6
occ:1.00
 OE2 B:GLU284 1.9 54.9 1.0
O4 B:OXL602 2.0 65.1 1.0
OD2 B:ASP308 2.4 53.9 1.0
O3 B:OXL602 2.4 63.5 1.0
O B:HOH733 2.6 60.5 1.0
C2 B:OXL602 2.7 65.0 1.0
C1 B:OXL602 2.9 64.1 1.0
CD B:GLU284 2.9 53.7 1.0
OE1 B:GLU284 3.2 55.4 1.0
CG B:ASP308 3.5 52.0 1.0
CB B:ASP308 3.9 46.0 1.0
O2 B:OXL602 3.9 65.5 1.0
O B:HOH893 3.9 78.7 1.0
NZ B:LYS282 4.0 50.0 1.0
O1 B:OXL602 4.1 63.8 1.0
CE B:LYS282 4.2 49.1 1.0
CG B:GLU284 4.3 48.4 1.0
O B:HOH831 4.5 53.0 1.0
CB B:ALA305 4.5 37.9 1.0
OD1 B:ASP308 4.6 53.5 1.0
N B:ASP308 4.7 41.9 1.0
CB B:GLU284 4.8 45.4 1.0
CE1 B:PHE256 4.9 56.7 1.0
CA B:ASP308 4.9 43.1 1.0

Magnesium binding site 3 out of 8 in 7frw

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Magnesium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:55.2
occ:1.00
 OE2 C:GLU284 1.9 41.4 1.0
O3 C:OXL603 2.1 69.3 1.0
OD2 C:ASP308 2.1 49.6 1.0
O4 C:OXL603 2.3 70.0 1.0
O C:HOH743 2.3 41.9 1.0
C1 C:OXL603 2.8 69.6 1.0
C2 C:OXL603 3.0 70.1 1.0
CD C:GLU284 3.0 39.8 1.0
CG C:ASP308 3.2 48.6 1.0
OE1 C:GLU284 3.3 39.6 1.0
CB C:ASP308 3.7 42.4 1.0
O C:HOH763 3.8 94.0 1.0
O1 C:OXL603 4.1 69.5 1.0
NZ C:LYS282 4.2 36.5 1.0
O2 C:OXL603 4.2 70.4 1.0
OD1 C:ASP308 4.3 50.7 1.0
CG C:GLU284 4.3 38.6 1.0
O C:HOH906 4.4 53.8 1.0
CE C:LYS282 4.4 35.8 1.0
N C:ASP308 4.5 38.5 1.0
CB C:ALA305 4.6 35.4 1.0
CA C:ASP308 4.7 39.6 1.0
CE1 C:PHE256 4.7 43.7 1.0
CB C:GLU284 4.8 36.5 1.0
CD1 C:PHE256 5.0 42.6 1.0

Magnesium binding site 4 out of 8 in 7frw

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Magnesium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:43.3
occ:1.00
 O D:HOH806 2.1 43.1 1.0
OD2 D:ASP308 2.1 47.5 1.0
OE2 D:GLU284 2.1 36.4 1.0
O1 D:OXL602 2.2 52.8 1.0
O2 D:OXL602 2.2 51.5 1.0
O D:HOH769 2.2 40.6 1.0
C1 D:OXL602 2.9 53.1 1.0
C2 D:OXL602 2.9 52.3 1.0
CD D:GLU284 3.1 36.5 1.0
CG D:ASP308 3.2 45.7 1.0
OE1 D:GLU284 3.5 34.3 1.0
CB D:ASP308 3.7 38.8 1.0
O D:HOH798 4.0 55.2 1.0
O4 D:OXL602 4.1 52.1 1.0
O3 D:OXL602 4.2 53.1 1.0
NZ D:LYS282 4.2 33.2 1.0
OD1 D:ASP308 4.2 47.9 1.0
O D:HOH831 4.4 37.1 1.0
N D:ASP308 4.4 35.1 1.0
CG D:GLU284 4.5 35.6 1.0
CE D:LYS282 4.5 30.9 1.0
CB D:ALA305 4.6 28.8 1.0
CA D:ASP308 4.7 36.1 1.0
CE1 D:PHE256 4.8 42.9 1.0
CB D:GLU284 4.9 34.2 1.0

Magnesium binding site 5 out of 8 in 7frw

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Magnesium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:63.8
occ:1.00
 OE2 E:GLU284 1.9 55.7 1.0
O3 E:OXL602 2.1 77.7 1.0
OD2 E:ASP308 2.2 53.3 1.0
O4 E:OXL602 2.3 77.2 1.0
C1 E:OXL602 2.8 77.8 1.0
C2 E:OXL602 2.9 77.3 1.0
CD E:GLU284 2.9 54.0 1.0
OE1 E:GLU284 3.3 53.8 1.0
CG E:ASP308 3.3 50.5 1.0
CB E:ASP308 3.8 45.1 1.0
O1 E:OXL602 4.0 78.1 1.0
NZ E:LYS282 4.0 51.7 1.0
O2 E:OXL602 4.1 77.0 1.0
O E:HOH870 4.1 57.7 1.0
CG E:GLU284 4.3 49.7 1.0
CE E:LYS282 4.3 50.0 1.0
OD1 E:ASP308 4.4 51.9 1.0
CB E:ALA305 4.5 41.3 1.0
N E:ASP308 4.6 41.4 1.0
CE1 E:PHE256 4.8 56.0 1.0
CB E:GLU284 4.8 45.4 1.0
CA E:ASP308 4.8 42.3 1.0
CD1 E:PHE256 5.0 55.4 1.0

Magnesium binding site 6 out of 8 in 7frw

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Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:49.1
occ:1.00
 OE2 F:GLU284 1.9 37.6 1.0
OD2 F:ASP308 2.0 44.1 1.0
O2 F:OXL602 2.3 53.9 1.0
O1 F:OXL602 2.3 52.4 1.0
O F:HOH784 2.4 50.7 1.0
CD F:GLU284 3.0 38.5 1.0
C1 F:OXL602 3.1 53.2 1.0
C2 F:OXL602 3.1 54.2 1.0
CG F:ASP308 3.1 41.5 1.0
OE1 F:GLU284 3.3 39.5 1.0
CB F:ASP308 3.6 35.1 1.0
O F:HOH1026 4.2 70.4 1.0
NZ F:LYS282 4.2 38.3 1.0
O F:HOH729 4.2 59.2 1.0
OD1 F:ASP308 4.2 43.4 1.0
O3 F:OXL602 4.2 52.7 1.0
O4 F:OXL602 4.3 54.6 1.0
CG F:GLU284 4.3 37.5 1.0
O F:HOH828 4.4 55.9 1.0
CE F:LYS282 4.5 37.9 1.0
N F:ASP308 4.5 32.2 1.0
CB F:ALA305 4.6 30.2 1.0
CE1 F:PHE256 4.7 45.2 1.0
CA F:ASP308 4.7 33.4 1.0
CB F:GLU284 4.7 34.2 1.0
CD1 F:PHE256 4.9 44.0 1.0

Magnesium binding site 7 out of 8 in 7frw

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Magnesium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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

b:40.7
occ:1.00
 OE2 G:GLU284 2.0 35.7 1.0
O1 G:OXL602 2.1 50.6 1.0
OD2 G:ASP308 2.2 42.9 1.0
O2 G:OXL602 2.2 51.3 1.0
O G:HOH786 2.3 43.7 1.0
O G:HOH780 2.3 42.6 1.0
C1 G:OXL602 2.9 50.9 1.0
C2 G:OXL602 2.9 51.4 1.0
CD G:GLU284 3.0 35.2 1.0
CG G:ASP308 3.2 42.3 1.0
OE1 G:GLU284 3.3 35.2 1.0
CB G:ASP308 3.7 36.0 1.0
O3 G:OXL602 4.1 50.8 1.0
NZ G:LYS282 4.1 33.8 1.0
O4 G:OXL602 4.2 51.3 1.0
CG G:GLU284 4.3 33.9 1.0
OD1 G:ASP308 4.3 44.9 1.0
O G:HOH944 4.4 45.8 1.0
O G:HOH1057 4.4 63.8 1.0
CE G:LYS282 4.4 33.4 1.0
N G:ASP308 4.5 34.2 1.0
CB G:ALA305 4.5 32.1 1.0
O G:HOH934 4.6 119.7 1.0
CA G:ASP308 4.7 34.3 1.0
CE1 G:PHE256 4.8 40.1 1.0
CB G:GLU284 4.8 31.2 1.0
CD1 G:PHE256 5.0 39.3 1.0

Magnesium binding site 8 out of 8 in 7frw

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Magnesium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 4


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 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg604

b:42.0
occ:1.00
 OE2 H:GLU284 2.0 29.6 1.0
OD2 H:ASP308 2.0 40.8 1.0
O4 H:OXL603 2.1 40.7 1.0
O3 H:OXL603 2.2 43.6 1.0
O H:HOH798 2.3 41.8 1.0
C2 H:OXL603 2.8 41.4 1.0
C1 H:OXL603 2.9 43.7 1.0
CD H:GLU284 3.1 29.8 1.0
CG H:ASP308 3.1 39.8 1.0
OE1 H:GLU284 3.5 30.9 1.0
CB H:ASP308 3.6 32.8 1.0
O2 H:OXL603 4.1 40.1 1.0
O1 H:OXL603 4.1 44.8 1.0
OD1 H:ASP308 4.2 43.0 1.0
NZ H:LYS282 4.2 31.0 1.0
N H:ASP308 4.3 28.3 1.0
CG H:GLU284 4.4 29.3 1.0
CE H:LYS282 4.5 30.2 1.0
CB H:ALA305 4.5 25.8 1.0
CA H:ASP308 4.6 29.8 1.0
CE1 H:PHE256 4.8 37.3 1.0
CB H:GLU284 4.8 29.0 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 21:36:47 2024

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