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Magnesium in PDB 7fs4: Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16, PDB code: 7fs4 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) 188.51 / 2.19
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.146, 113.021, 188.617, 90, 91.93, 90
R / Rfree (%) 20.7 / 23.6

Other elements in 7fs4:

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16 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 16 (pdb code 7fs4). 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 16, PDB code: 7fs4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7fs4

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Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16


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

b:46.6
occ:1.00
 OD2 A:ASP308 2.0 70.4 1.0
O1 A:OXL602 2.0 74.8 1.0
O2 A:OXL602 2.1 75.1 1.0
OE2 A:GLU284 2.3 71.5 1.0
C1 A:OXL602 2.7 74.8 1.0
C2 A:OXL602 2.8 75.0 1.0
CG A:ASP308 3.1 68.8 1.0
CD A:GLU284 3.4 71.8 1.0
OE1 A:GLU284 3.7 74.7 1.0
CB A:ASP308 3.8 64.5 1.0
O3 A:OXL602 4.0 74.7 1.0
O4 A:OXL602 4.0 75.0 1.0
OD1 A:ASP308 4.1 69.7 1.0
NZ A:LYS282 4.3 65.1 1.0
N A:ASP308 4.4 61.8 1.0
CG A:GLU284 4.7 65.9 1.0
CA A:ASP308 4.7 62.8 1.0
CE A:LYS282 4.7 64.0 1.0
CE1 A:PHE256 4.9 72.4 1.0
CB A:ALA305 4.9 55.7 1.0

Magnesium binding site 2 out of 8 in 7fs4

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Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16


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

b:37.3
occ:1.00
 OD2 B:ASP308 1.9 56.6 1.0
O4 B:OXL602 1.9 52.5 1.0
OE2 B:GLU284 1.9 67.7 1.0
O3 B:OXL602 2.5 50.5 1.0
C2 B:OXL602 2.8 52.4 1.0
CD B:GLU284 3.0 65.5 1.0
C1 B:OXL602 3.0 50.9 1.0
CG B:ASP308 3.0 53.7 1.0
OE1 B:GLU284 3.4 67.4 1.0
CB B:ASP308 3.6 48.3 1.0
O2 B:OXL602 4.0 53.2 1.0
OD1 B:ASP308 4.1 53.6 1.0
O1 B:OXL602 4.2 50.1 1.0
NZ B:LYS282 4.3 62.5 1.0
CG B:GLU284 4.3 57.4 1.0
N B:ASP308 4.4 44.0 1.0
O B:HOH793 4.5 71.0 1.0
CE1 B:PHE256 4.6 57.9 1.0
CA B:ASP308 4.6 45.5 1.0
CE B:LYS282 4.6 60.2 1.0
CB B:ALA305 4.7 43.4 1.0
CB B:GLU284 4.7 52.9 1.0
CD1 B:PHE256 4.9 57.1 1.0

Magnesium binding site 3 out of 8 in 7fs4

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Magnesium binding site 3 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16


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

b:34.2
occ:1.00
 OE2 C:GLU284 1.9 47.4 1.0
O3 C:OXL603 1.9 65.8 1.0
O4 C:OXL603 2.1 66.6 1.0
OD2 C:ASP308 2.1 63.8 1.0
C1 C:OXL603 2.7 65.6 1.0
C2 C:OXL603 2.8 66.2 1.0
CD C:GLU284 2.9 50.8 1.0
OE1 C:GLU284 3.3 54.4 1.0
CG C:ASP308 3.3 61.6 1.0
CB C:ASP308 3.9 54.5 1.0
O1 C:OXL603 4.0 65.0 1.0
NZ C:LYS282 4.0 44.3 1.0
O2 C:OXL603 4.0 66.1 1.0
CG C:GLU284 4.3 49.7 1.0
OD1 C:ASP308 4.3 63.8 1.0
CE C:LYS282 4.4 44.2 1.0
N C:ASP308 4.6 50.5 1.0
CB C:ALA305 4.7 46.1 1.0
CE1 C:PHE256 4.7 49.3 1.0
CB C:GLU284 4.8 48.9 1.0
CA C:ASP308 4.9 52.1 1.0
CD1 C:PHE256 4.9 48.3 1.0

Magnesium binding site 4 out of 8 in 7fs4

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Magnesium binding site 4 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16


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

b:27.9
occ:1.00
 OD2 D:ASP308 1.9 49.0 1.0
O1 D:OXL602 2.0 55.0 1.0
OE2 D:GLU284 2.1 50.5 1.0
O2 D:OXL602 2.1 53.9 1.0
C1 D:OXL602 2.8 54.3 1.0
C2 D:OXL602 2.9 54.1 1.0
CG D:ASP308 3.1 47.2 1.0
CD D:GLU284 3.2 50.3 1.0
OE1 D:GLU284 3.6 52.7 1.0
CB D:ASP308 3.7 43.3 1.0
O4 D:OXL602 4.1 54.0 1.0
O D:HOH885 4.1 48.6 1.0
OD1 D:ASP308 4.1 47.5 1.0
O3 D:OXL602 4.1 53.7 1.0
NZ D:LYS282 4.2 42.4 1.0
N D:ASP308 4.4 40.7 1.0
CG D:GLU284 4.5 45.3 1.0
CE D:LYS282 4.6 38.7 1.0
CA D:ASP308 4.7 41.9 1.0
CB D:ALA305 4.7 32.4 1.0
CE1 D:PHE256 4.8 46.3 1.0
CB D:GLU284 4.9 41.8 1.0

Magnesium binding site 5 out of 8 in 7fs4

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Magnesium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16


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

b:41.2
occ:1.00
 O3 E:OXL602 1.9 75.7 1.0
OD2 E:ASP308 1.9 62.8 1.0
OE2 E:GLU284 2.0 63.9 1.0
O4 E:OXL602 2.3 75.5 1.0
C1 E:OXL602 2.7 75.6 1.0
C2 E:OXL602 2.9 75.5 1.0
CD E:GLU284 3.0 63.7 1.0
CG E:ASP308 3.1 61.0 1.0
OE1 E:GLU284 3.4 66.2 1.0
CB E:ASP308 3.7 55.8 1.0
O1 E:OXL602 4.0 75.4 1.0
O2 E:OXL602 4.1 75.2 1.0
OD1 E:ASP308 4.1 62.5 1.0
NZ E:LYS282 4.2 55.2 1.0
CG E:GLU284 4.3 58.1 1.0
N E:ASP308 4.4 52.1 1.0
CE E:LYS282 4.6 54.1 1.0
CA E:ASP308 4.6 53.1 1.0
CB E:ALA305 4.7 52.8 1.0
CE1 E:PHE256 4.7 65.9 1.0
CB E:GLU284 4.8 53.6 1.0
CD1 E:PHE256 5.0 65.0 1.0

Magnesium binding site 6 out of 8 in 7fs4

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Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16


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

b:27.3
occ:1.00
 OD2 F:ASP308 1.9 48.7 1.0
O2 F:OXL602 2.0 57.9 1.0
OE2 F:GLU284 2.2 45.3 1.0
O1 F:OXL602 2.3 56.4 1.0
C2 F:OXL602 2.9 57.5 1.0
C1 F:OXL602 3.0 56.5 1.0
CG F:ASP308 3.1 47.1 1.0
CD F:GLU284 3.2 48.9 1.0
OE1 F:GLU284 3.6 52.7 1.0
CB F:ASP308 3.7 41.5 1.0
O4 F:OXL602 4.0 57.5 1.0
OD1 F:ASP308 4.1 48.3 1.0
O3 F:OXL602 4.2 55.9 1.0
NZ F:LYS282 4.2 40.6 1.0
O F:HOH858 4.3 66.2 1.0
N F:ASP308 4.4 39.2 1.0
CG F:GLU284 4.6 44.7 1.0
CE F:LYS282 4.6 38.3 1.0
CA F:ASP308 4.7 39.9 1.0
CB F:ALA305 4.8 36.8 1.0
CE1 F:PHE256 4.8 53.4 1.0
CB F:GLU284 5.0 42.5 1.0

Magnesium binding site 7 out of 8 in 7fs4

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Magnesium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16


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

b:20.0
occ:1.00
 O2 G:OXL602 2.0 54.0 1.0
OE2 G:GLU284 2.0 41.6 1.0
O1 G:OXL602 2.0 52.2 1.0
OD2 G:ASP308 2.1 54.5 1.0
O G:HOH783 2.2 49.6 1.0
O G:HOH761 2.2 40.5 1.0
C2 G:OXL602 2.7 53.6 1.0
C1 G:OXL602 2.7 52.7 1.0
CD G:GLU284 3.0 42.8 1.0
CG G:ASP308 3.2 52.1 1.0
OE1 G:GLU284 3.4 44.8 1.0
CB G:ASP308 3.8 45.9 1.0
O3 G:OXL602 3.9 52.5 1.0
O4 G:OXL602 4.0 53.6 1.0
NZ G:LYS282 4.1 39.7 1.0
O G:HOH860 4.2 57.6 1.0
OD1 G:ASP308 4.2 53.8 1.0
CG G:GLU284 4.4 39.5 1.0
N G:ASP308 4.5 43.2 1.0
CE G:LYS282 4.5 36.0 1.0
CB G:ALA305 4.7 39.2 1.0
CE1 G:PHE256 4.7 41.1 1.0
CA G:ASP308 4.7 43.7 1.0
CB G:GLU284 4.8 38.1 1.0
CD1 G:PHE256 5.0 40.1 1.0

Magnesium binding site 8 out of 8 in 7fs4

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Magnesium binding site 8 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 16


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

b:20.6
occ:1.00
 OE2 H:GLU284 1.9 42.0 1.0
OD2 H:ASP308 1.9 44.6 1.0
O3 H:OXL602 2.0 44.4 1.0
O H:HOH708 2.0 43.4 1.0
O4 H:OXL602 2.1 44.3 1.0
O H:HOH720 2.1 29.5 1.0
C2 H:OXL602 2.8 44.4 1.0
C1 H:OXL602 2.9 44.5 1.0
CD H:GLU284 3.0 42.4 1.0
CG H:ASP308 3.0 42.8 1.0
OE1 H:GLU284 3.4 44.6 1.0
CB H:ASP308 3.6 37.2 1.0
O1 H:OXL602 4.1 44.7 1.0
O2 H:OXL602 4.1 44.2 1.0
OD1 H:ASP308 4.1 44.5 1.0
O H:HOH913 4.2 49.9 1.0
NZ H:LYS282 4.2 27.3 1.0
CG H:GLU284 4.3 37.9 1.0
N H:ASP308 4.3 35.9 1.0
O H:HOH928 4.4 62.6 1.0
CE H:LYS282 4.5 26.8 1.0
CA H:ASP308 4.6 37.0 1.0
CB H:ALA305 4.6 29.1 1.0
CE1 H:PHE256 4.6 42.7 1.0
CB H:GLU284 4.7 36.0 1.0
CD1 H:PHE256 5.0 41.9 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 21:41:59 2024

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