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Magnesium in PDB 5wsa: Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate

Enzymatic activity of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate

All present enzymatic activity of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate:
2.7.1.40;

Protein crystallography data

The structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate, PDB code: 5wsa was solved by W.Zhong, Q.Cai, A.El Sahili, J.Lescar, P.C.Dedon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.71 / 2.85
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 125.420, 125.420, 144.192, 90.00, 90.00, 120.00
R / Rfree (%) 15.1 / 19.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate (pdb code 5wsa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate, PDB code: 5wsa:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5wsa

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Magnesium binding site 1 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:27.0
occ:1.00
 O A:HOH602 1.8 25.5 1.0
OD2 A:ASP244 1.9 36.3 1.0
O4 A:OXL503 2.2 27.8 1.0
OE1 A:GLU220 2.3 37.4 1.0
O1 A:OXL503 2.3 28.5 1.0
C2 A:OXL503 2.8 28.5 1.0
C1 A:OXL503 2.9 26.5 1.0
CG A:ASP244 3.1 36.5 1.0
CD A:GLU220 3.2 35.6 1.0
OE2 A:GLU220 3.5 33.2 1.0
NZ A:LYS218 3.7 34.3 1.0
CB A:ASP244 3.8 35.2 1.0
O2 A:OXL503 3.9 24.2 1.0
OD1 A:ASP244 4.1 38.0 1.0
O3 A:OXL503 4.1 25.3 1.0
CZ A:PHE192 4.3 38.4 1.0
N A:ASP244 4.5 36.2 1.0
CE A:LYS218 4.5 35.9 1.0
CG A:GLU220 4.6 35.4 1.0
CE2 A:PHE192 4.7 38.6 1.0
CA A:ASP244 4.7 35.4 1.0
CE1 A:PHE192 4.8 38.6 1.0
CB A:ALA241 4.8 32.2 1.0
CB A:GLU220 5.0 35.8 1.0

Magnesium binding site 2 out of 4 in 5wsa

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Magnesium binding site 2 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:25.7
occ:1.00
 OD2 B:ASP244 2.0 34.1 1.0
OE1 B:GLU220 2.1 35.1 1.0
O B:HOH601 2.1 7.3 1.0
O3 B:OXL503 2.2 17.4 1.0
O4 B:OXL503 2.4 26.9 1.0
C2 B:OXL503 2.6 24.6 1.0
C1 B:OXL503 2.7 19.9 1.0
CG B:ASP244 3.1 33.9 1.0
CD B:GLU220 3.1 31.5 1.0
OE2 B:GLU220 3.4 29.9 1.0
NZ B:LYS218 3.6 40.6 1.0
O2 B:OXL503 3.6 20.4 1.0
CB B:ASP244 3.7 34.0 1.0
O1 B:OXL503 3.9 17.2 1.0
OD1 B:ASP244 4.1 32.4 1.0
CE B:LYS218 4.3 41.0 1.0
CZ B:PHE192 4.4 32.6 1.0
N B:ASP244 4.4 33.4 1.0
CG B:GLU220 4.5 31.8 1.0
CB B:ALA241 4.6 26.8 1.0
CA B:ASP244 4.7 34.6 1.0
CB B:GLU220 4.8 31.6 1.0
CE2 B:PHE192 4.8 33.0 1.0
CE1 B:PHE192 4.8 33.1 1.0
O B:HOH617 4.9 37.5 1.0

Magnesium binding site 3 out of 4 in 5wsa

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Magnesium binding site 3 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:24.5
occ:1.00
 O C:HOH602 1.6 31.1 1.0
OD2 C:ASP244 1.8 53.1 1.0
O1 C:OXL503 2.2 47.9 1.0
OE1 C:GLU220 2.3 44.9 1.0
O4 C:OXL503 2.4 21.9 1.0
O C:HOH605 2.5 27.8 1.0
C1 C:OXL503 2.8 44.4 1.0
C2 C:OXL503 2.9 31.6 1.0
CG C:ASP244 3.0 48.8 1.0
CD C:GLU220 3.3 41.9 1.0
OE2 C:GLU220 3.5 40.0 1.0
CB C:ASP244 3.7 48.3 1.0
O3 C:OXL503 4.0 43.5 1.0
OD1 C:ASP244 4.0 45.6 1.0
O2 C:OXL503 4.0 33.8 1.0
CZ C:PHE192 4.1 46.8 1.0
NZ C:LYS218 4.1 42.8 1.0
CE C:LYS218 4.5 43.3 1.0
N C:ASP244 4.5 45.9 1.0
CE2 C:PHE192 4.5 48.1 1.0
CG C:GLU220 4.7 41.7 1.0
CE1 C:PHE192 4.7 46.9 1.0
CA C:ASP244 4.7 46.1 1.0

Magnesium binding site 4 out of 4 in 5wsa

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Magnesium binding site 4 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate and Allosteric Activator Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:33.2
occ:1.00
 O D:HOH603 1.8 33.1 1.0
OD2 D:ASP244 1.9 40.4 1.0
O3 D:OXL503 2.0 46.4 1.0
OE1 D:GLU220 2.3 43.3 1.0
O2 D:OXL503 2.7 15.3 1.0
C1 D:OXL503 2.9 35.4 1.0
CG D:ASP244 3.0 39.0 1.0
C2 D:OXL503 3.1 24.3 1.0
CD D:GLU220 3.2 42.9 1.0
OE2 D:GLU220 3.4 44.3 1.0
CB D:ASP244 3.8 38.8 1.0
OD1 D:ASP244 4.0 38.5 1.0
CZ D:PHE192 4.0 40.2 1.0
O1 D:OXL503 4.0 38.3 1.0
NZ D:LYS218 4.1 40.6 1.0
O4 D:OXL503 4.2 24.6 1.0
CE2 D:PHE192 4.4 40.8 1.0
CE D:LYS218 4.5 42.1 1.0
CE1 D:PHE192 4.5 40.4 1.0
CG D:GLU220 4.6 42.5 1.0
N D:ASP244 4.7 38.1 1.0
CA D:ASP244 4.8 38.1 1.0
CB D:GLU220 4.9 40.7 1.0
CB D:ALA241 5.0 39.5 1.0

Reference:

W.Zhong, L.Cui, B.C.Goh, Q.Cai, P.Ho, Y.H.Chionh, M.Yuan, A.E.Sahili, L.A.Fothergill-Gilmore, M.D.Walkinshaw, J.Lescar, P.C.Dedon. Allosteric Pyruvate Kinase-Based "Logic Gate" Synergistically Senses Energy and Sugar Levels in Mycobacterium Tuberculosis. Nat Commun V. 8 1986 2017.
ISSN: ESSN 2041-1723
PubMed: 29215013
DOI: 10.1038/S41467-017-02086-Y
Page generated: Mon Sep 30 08:19:50 2024

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