Magnesium in PDB 8xfd: Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348)

Enzymatic activity of Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348)

All present enzymatic activity of Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348):
2.7.1.40;

Protein crystallography data

The structure of Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348), PDB code: 8xfd was solved by R.Sun, A.Achour, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.43 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 84.93, 86.962, 91.554, 76.78, 66.88, 80.22
R / Rfree (%) 23.2 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348) (pdb code 8xfd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348), PDB code: 8xfd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8xfd

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Magnesium binding site 1 out of 4 in the Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:36.4
occ:1.00
 OE1 A:GLU282 2.2 21.8 1.0
OD2 A:ASP306 2.3 28.7 1.0
O A:HOH822 2.9 26.2 1.0
CG A:ASP306 3.1 19.8 1.0
CD A:GLU282 3.2 18.6 1.0
O A:HOH762 3.3 28.7 1.0
OE2 A:GLU282 3.6 17.4 1.0
CB A:ASP306 3.8 14.2 1.0
OD1 A:ASP306 3.9 26.5 1.0
O A:HOH820 3.9 13.9 1.0
NZ A:LYS280 4.2 13.8 1.0
CG A:GLU282 4.5 20.4 1.0
CE A:LYS280 4.7 18.0 1.0
OG A:SER253 4.8 16.7 1.0
N A:ASP306 4.9 14.9 1.0
O A:HOH857 4.9 31.1 1.0
CA A:ASP306 5.0 18.6 1.0
O A:HOH763 5.0 22.1 1.0
CB A:GLU282 5.0 20.8 1.0

Magnesium binding site 2 out of 4 in 8xfd

Go back to Magnesium Binding Sites List in 8xfd
Magnesium binding site 2 out of 4 in the Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:33.6
occ:1.00
 OD2 B:ASP306 2.0 37.3 1.0
OE2 B:GLU282 2.3 33.8 1.0
CG B:ASP306 3.2 31.1 1.0
CD B:GLU282 3.3 35.2 1.0
OE1 B:GLU282 3.5 28.7 1.0
O B:HOH855 3.6 30.8 1.0
O B:HOH847 3.6 32.5 1.0
CB B:ASP306 4.0 27.0 1.0
OD1 B:ASP306 4.0 35.9 1.0
O B:HOH892 4.2 32.5 1.0
O B:HOH848 4.2 33.0 1.0
CG B:GLU282 4.7 30.9 1.0
O B:HOH849 4.7 33.1 1.0
NZ B:LYS280 4.9 26.4 1.0
OG B:SER253 5.0 34.2 1.0

Magnesium binding site 3 out of 4 in 8xfd

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Magnesium binding site 3 out of 4 in the Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:41.2
occ:1.00
 OD2 C:ASP306 1.9 39.6 1.0
OE2 C:GLU282 2.2 33.2 1.0
O C:HOH803 2.6 31.9 1.0
O C:HOH723 2.9 24.8 1.0
CG C:ASP306 3.0 41.4 1.0
CD C:GLU282 3.2 30.6 1.0
OE1 C:GLU282 3.5 31.2 1.0
O C:HOH782 3.7 33.3 1.0
CB C:ASP306 3.8 28.4 1.0
OD1 C:ASP306 4.0 38.9 1.0
O C:HOH707 4.2 37.4 1.0
CG C:GLU282 4.5 30.6 1.0
O C:HOH843 4.5 43.8 1.0
O C:HOH831 4.5 27.4 1.0
CB C:GLU282 4.6 30.4 1.0

Magnesium binding site 4 out of 4 in 8xfd

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Magnesium binding site 4 out of 4 in the Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Pyruvate Kinase Tetramer in Complex with Allosteric Activator, Mitapivat (Mtpv, Ag-348) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:30.1
occ:1.00
 OD2 D:ASP306 2.1 24.2 1.0
OE1 D:GLU282 2.2 24.4 1.0
CD D:GLU282 3.1 19.1 1.0
OE2 D:GLU282 3.3 17.1 1.0
CG D:ASP306 3.3 22.2 1.0
O D:HOH807 3.5 23.2 1.0
O D:HOH836 4.0 20.7 1.0
CB D:ASP306 4.1 17.9 1.0
OD1 D:ASP306 4.3 24.0 1.0
CG D:GLU282 4.4 18.9 1.0
O D:HOH781 4.6 23.4 1.0
CB D:GLU282 4.7 15.1 1.0
OG D:SER253 4.8 18.3 1.0
O D:HOH893 4.9 29.7 1.0
CB D:SER253 4.9 18.3 1.0

Reference:

X.Han, T.Sandalova, C.Zhang, A.Mardinoglu, A.Achour, R.Sun. High Resolution Crystal Structure of the Pyruvate Kinase Tetramer in Complex with the Allosteric Activator Mitapivat/Ag-348 Crystals 2024.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST14050441
Page generated: Sat Oct 5 01:04:25 2024

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