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Magnesium in PDB 7frv: Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 3

Enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 3

All present enzymatic activity of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 3:
2.7.1.40;

Protein crystallography data

The structure of Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 3, PDB code: 7frv 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) 188.34 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 208.043, 112.707, 188.415, 90, 91.59, 90
R / Rfree (%) 20.6 / 23.2

Other elements in 7frv:

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

Magnesium binding site 1 out of 8 in 7frv

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Magnesium binding site 1 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 3


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

b:84.9
occ:1.00
 O2 A:OXL602 2.0 85.9 1.0
O1 A:OXL602 2.3 85.2 1.0
OE2 A:GLU284 2.3 68.9 1.0
OD2 A:ASP308 2.4 66.1 1.0
C2 A:OXL602 2.8 85.9 1.0
C1 A:OXL602 2.9 85.5 1.0
CD A:GLU284 3.2 67.6 1.0
OE1 A:GLU284 3.4 70.0 1.0
CG A:ASP308 3.5 63.5 1.0
NZ A:LYS282 3.9 63.5 1.0
O4 A:OXL602 4.0 86.0 1.0
O3 A:OXL602 4.1 85.3 1.0
CB A:ASP308 4.2 57.9 1.0
CE A:LYS282 4.4 62.1 1.0
OD1 A:ASP308 4.5 64.1 1.0
CG A:GLU284 4.6 60.3 1.0
CB A:ALA305 4.9 51.2 1.0
N A:ASP308 4.9 53.9 1.0
CE1 A:PHE256 4.9 62.1 1.0
OG A:SER255 5.0 63.0 1.0

Magnesium binding site 2 out of 8 in 7frv

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Magnesium binding site 2 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 3


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

b:85.7
occ:1.00
 O4 B:OXL602 2.0 69.4 1.0
OE2 B:GLU284 2.0 58.2 1.0
OD2 B:ASP308 2.5 56.5 1.0
CD B:GLU284 2.8 56.0 1.0
OE1 B:GLU284 2.8 58.6 1.0
O B:HOH743 2.9 58.1 1.0
C2 B:OXL602 3.0 69.2 1.0
O3 B:OXL602 3.0 67.6 1.0
C1 B:OXL602 3.5 68.0 1.0
CG B:ASP308 3.6 54.5 1.0
NZ B:LYS282 3.8 61.5 1.0
O B:HOH811 3.9 57.2 1.0
O B:HOH840 4.0 65.0 1.0
O2 B:OXL602 4.1 69.6 1.0
CE B:LYS282 4.2 59.0 1.0
CB B:ASP308 4.2 48.4 1.0
CG B:GLU284 4.2 50.7 1.0
O B:HOH779 4.5 106.4 1.0
CE1 B:PHE256 4.6 57.6 1.0
CD1 B:PHE256 4.6 56.9 1.0
OG B:SER255 4.6 54.5 1.0
OD1 B:ASP308 4.7 55.6 1.0
O1 B:OXL602 4.7 67.5 1.0
CB B:GLU284 4.8 46.8 1.0
CB B:ALA305 4.8 39.9 1.0
CB B:SER255 4.9 54.4 1.0

Magnesium binding site 3 out of 8 in 7frv

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


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

b:64.7
occ:1.00
 OE2 C:GLU284 1.9 45.7 1.0
O C:HOH778 2.1 48.8 1.0
O4 C:OXL602 2.2 77.5 1.0
O3 C:OXL602 2.2 76.7 1.0
OD2 C:ASP308 2.2 56.1 1.0
O C:HOH781 2.3 55.0 1.0
CD C:GLU284 2.9 45.6 1.0
C1 C:OXL602 2.9 77.0 1.0
C2 C:OXL602 2.9 77.5 1.0
OE1 C:GLU284 3.2 45.1 1.0
CG C:ASP308 3.4 54.2 1.0
O C:HOH759 3.8 84.5 1.0
CB C:ASP308 3.9 47.5 1.0
NZ C:LYS282 3.9 48.2 1.0
O2 C:OXL602 4.1 77.6 1.0
O1 C:OXL602 4.2 76.7 1.0
CG C:GLU284 4.3 45.4 1.0
CE C:LYS282 4.3 45.9 1.0
O C:HOH839 4.3 49.2 1.0
OD1 C:ASP308 4.4 56.7 1.0
CB C:ALA305 4.6 38.8 1.0
N C:ASP308 4.7 44.1 1.0
CE1 C:PHE256 4.8 43.0 1.0
CB C:GLU284 4.8 42.5 1.0
CA C:ASP308 4.9 45.2 1.0
CD1 C:PHE256 4.9 42.3 1.0

Magnesium binding site 4 out of 8 in 7frv

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


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

b:54.8
occ:1.00
 OD2 D:ASP308 2.1 49.8 1.0
O D:HOH826 2.1 44.3 1.0
OE2 D:GLU284 2.1 42.4 1.0
O2 D:OXL602 2.3 58.2 1.0
O1 D:OXL602 2.3 59.8 1.0
C1 D:OXL602 3.0 59.7 1.0
C2 D:OXL602 3.1 58.6 1.0
CD D:GLU284 3.1 41.0 1.0
CG D:ASP308 3.2 47.7 1.0
OE1 D:GLU284 3.4 40.4 1.0
CB D:ASP308 3.9 41.0 1.0
NZ D:LYS282 4.1 33.1 1.0
OD1 D:ASP308 4.2 49.5 1.0
O4 D:OXL602 4.3 57.9 1.0
O D:HOH778 4.3 36.9 1.0
O3 D:OXL602 4.3 59.7 1.0
CG D:GLU284 4.5 38.9 1.0
CE D:LYS282 4.5 32.4 1.0
N D:ASP308 4.6 37.1 1.0
CB D:ALA305 4.7 32.2 1.0
CE1 D:PHE256 4.8 43.1 1.0
CA D:ASP308 4.9 38.5 1.0
CB D:GLU284 4.9 37.2 1.0
O D:HOH958 4.9 65.8 1.0
CD1 D:PHE256 5.0 42.0 1.0

Magnesium binding site 5 out of 8 in 7frv

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Magnesium binding site 5 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 3


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

b:68.5
occ:1.00
 O3 E:OXL602 1.9 76.4 1.0
OE2 E:GLU284 2.1 60.1 1.0
OD2 E:ASP308 2.2 56.2 1.0
O4 E:OXL602 2.3 75.6 1.0
C1 E:OXL602 2.7 76.3 1.0
C2 E:OXL602 2.9 75.9 1.0
CD E:GLU284 3.1 59.0 1.0
CG E:ASP308 3.3 53.8 1.0
OE1 E:GLU284 3.4 59.0 1.0
CB E:ASP308 3.9 49.5 1.0
O1 E:OXL602 4.0 76.4 1.0
NZ E:LYS282 4.0 53.5 1.0
O2 E:OXL602 4.1 75.7 1.0
OD1 E:ASP308 4.3 54.5 1.0
CE E:LYS282 4.5 52.4 1.0
CG E:GLU284 4.5 55.1 1.0
N E:ASP308 4.6 46.6 1.0
CB E:ALA305 4.6 47.1 1.0
CA E:ASP308 4.9 47.7 1.0
CE1 E:PHE256 4.9 61.4 1.0
CB E:GLU284 4.9 51.0 1.0

Magnesium binding site 6 out of 8 in 7frv

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Magnesium binding site 6 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 3


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

b:51.9
occ:1.00
 OD2 F:ASP308 2.1 48.6 1.0
OE2 F:GLU284 2.1 41.3 1.0
O F:HOH744 2.3 41.8 1.0
O2 F:OXL602 2.3 66.7 1.0
O1 F:OXL602 2.3 65.5 1.0
CD F:GLU284 3.1 41.3 1.0
C1 F:OXL602 3.1 65.8 1.0
C2 F:OXL602 3.1 67.0 1.0
CG F:ASP308 3.2 46.2 1.0
OE1 F:GLU284 3.4 43.3 1.0
CB F:ASP308 3.8 38.3 1.0
O F:HOH892 4.0 56.9 1.0
O F:HOH730 4.1 68.4 1.0
NZ F:LYS282 4.1 39.8 1.0
O F:HOH921 4.2 69.8 1.0
OD1 F:ASP308 4.2 48.9 1.0
O3 F:OXL602 4.3 65.2 1.0
O4 F:OXL602 4.3 67.4 1.0
CG F:GLU284 4.4 40.4 1.0
CE F:LYS282 4.5 39.4 1.0
N F:ASP308 4.6 34.9 1.0
CB F:ALA305 4.7 34.0 1.0
CE1 F:PHE256 4.8 49.2 1.0
CA F:ASP308 4.8 35.8 1.0
CB F:GLU284 4.9 37.8 1.0
CD1 F:PHE256 5.0 48.0 1.0

Magnesium binding site 7 out of 8 in 7frv

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Magnesium binding site 7 out of 8 in the Structure of Liver Pyruvate Kinase in Complex with Allosteric Modulator 3


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 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg604

b:46.9
occ:1.00
 OE2 G:GLU284 2.0 41.0 1.0
OD2 G:ASP308 2.1 47.7 1.0
O2 G:OXL603 2.1 63.9 1.0
O1 G:OXL603 2.2 62.8 1.0
O G:HOH750 2.2 48.4 1.0
O G:HOH764 2.3 46.7 1.0
C2 G:OXL603 2.8 63.7 1.0
C1 G:OXL603 2.9 62.9 1.0
CD G:GLU284 3.0 40.5 1.0
CG G:ASP308 3.2 46.8 1.0
OE1 G:GLU284 3.3 42.6 1.0
CB G:ASP308 3.8 41.2 1.0
O3 G:OXL603 4.0 62.3 1.0
O4 G:OXL603 4.1 63.8 1.0
NZ G:LYS282 4.1 37.6 1.0
OD1 G:ASP308 4.3 49.5 1.0
CG G:GLU284 4.4 39.1 1.0
CE G:LYS282 4.5 35.7 1.0
N G:ASP308 4.6 39.5 1.0
CB G:ALA305 4.7 36.1 1.0
CE1 G:PHE256 4.7 42.5 1.0
CA G:ASP308 4.8 39.7 1.0
CB G:GLU284 4.8 37.2 1.0
O G:HOH898 4.9 63.4 1.0
CD1 G:PHE256 4.9 41.8 1.0

Magnesium binding site 8 out of 8 in 7frv

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


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

b:44.4
occ:1.00
 OD2 H:ASP308 2.0 44.7 1.0
OE2 H:GLU284 2.0 36.2 1.0
O4 H:OXL602 2.1 50.1 1.0
O3 H:OXL602 2.2 51.5 1.0
O H:HOH747 2.3 35.7 1.0
O H:HOH783 2.4 49.3 1.0
C2 H:OXL602 2.7 50.8 1.0
C1 H:OXL602 2.8 51.8 1.0
CD H:GLU284 3.0 35.1 1.0
CG H:ASP308 3.1 42.7 1.0
OE1 H:GLU284 3.5 34.0 1.0
CB H:ASP308 3.6 36.5 1.0
O2 H:OXL602 4.0 50.4 1.0
O1 H:OXL602 4.1 52.1 1.0
OD1 H:ASP308 4.1 45.5 1.0
NZ H:LYS282 4.2 34.7 1.0
N H:ASP308 4.3 32.6 1.0
CG H:GLU284 4.3 34.0 1.0
O H:HOH885 4.4 40.6 1.0
CB H:ALA305 4.5 27.8 1.0
CA H:ASP308 4.5 34.2 1.0
CE H:LYS282 4.6 34.0 1.0
CB H:GLU284 4.7 31.7 1.0
CE1 H:PHE256 4.7 37.7 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 21:36:15 2024

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