Magnesium in PDB 5wsc: Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and Glucose 6-Phosphate

Enzymatic activity of Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and Glucose 6-Phosphate

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

Protein crystallography data

The structure of Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and Glucose 6-Phosphate, PDB code: 5wsc 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) 53.85 / 2.40
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 124.370, 124.370, 144.192, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 22.7

Other elements in 5wsc:

The structure of Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and Glucose 6-Phosphate also contains other interesting chemical elements:

Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and Glucose 6-Phosphate (pdb code 5wsc). 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 of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and Glucose 6-Phosphate, PDB code: 5wsc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5wsc

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Magnesium binding site 1 out of 4 in the Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and 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 Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:22.0
occ:1.00
 O A:HOH629 2.1 18.7 1.0
O4 A:OXL504 2.1 18.5 1.0
OD2 A:ASP244 2.1 24.7 1.0
O3 A:OXL504 2.2 20.0 1.0
O A:HOH604 2.2 20.2 1.0
OE1 A:GLU220 2.2 21.3 1.0
C2 A:OXL504 2.8 19.6 1.0
C1 A:OXL504 2.9 21.2 1.0
CD A:GLU220 3.1 22.5 1.0
CG A:ASP244 3.2 23.6 1.0
OE2 A:GLU220 3.4 20.2 1.0
NZ A:LYS218 3.7 22.4 1.0
CB A:ASP244 3.7 24.4 1.0
O2 A:OXL504 4.1 23.0 1.0
O1 A:OXL504 4.1 20.3 1.0
CE A:LYS218 4.2 22.8 1.0
OD1 A:ASP244 4.3 24.5 1.0
CB A:ALA241 4.5 20.6 1.0
CG A:GLU220 4.5 23.7 1.0
CZ A:PHE192 4.6 23.7 1.0
N A:ASP244 4.6 23.2 1.0
O A:HOH640 4.8 17.3 1.0
CA A:ASP244 4.8 23.3 1.0
CB A:GLU220 4.8 23.8 1.0
CE1 A:PHE192 5.0 26.9 1.0
CE2 A:PHE192 5.0 24.8 1.0

Magnesium binding site 2 out of 4 in 5wsc

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Magnesium binding site 2 out of 4 in the Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and 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 Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:23.0
occ:1.00
 O B:HOH629 2.0 14.8 1.0
OD2 B:ASP244 2.0 24.0 1.0
O4 B:OXL504 2.1 20.1 1.0
O3 B:OXL504 2.1 18.8 1.0
OE1 B:GLU220 2.2 20.0 1.0
O B:HOH664 2.3 19.7 1.0
C2 B:OXL504 2.8 18.6 1.0
C1 B:OXL504 2.8 20.7 1.0
CG B:ASP244 3.0 24.2 1.0
CD B:GLU220 3.2 23.0 1.0
CB B:ASP244 3.5 24.7 1.0
OE2 B:GLU220 3.6 19.1 1.0
NZ B:LYS218 4.0 20.6 1.0
O2 B:OXL504 4.1 21.6 1.0
O1 B:OXL504 4.1 21.1 1.0
OD1 B:ASP244 4.1 25.8 1.0
N B:ASP244 4.3 23.7 1.0
CZ B:PHE192 4.4 24.5 1.0
CE B:LYS218 4.5 21.1 1.0
CA B:ASP244 4.5 23.7 1.0
CG B:GLU220 4.5 23.5 1.0
CB B:ALA241 4.6 19.1 1.0
CE1 B:PHE192 4.8 25.8 1.0
CB B:GLU220 4.8 23.4 1.0
O B:ALA241 4.9 23.2 1.0
CE2 B:PHE192 5.0 25.6 1.0

Magnesium binding site 3 out of 4 in 5wsc

Go back to Magnesium Binding Sites List in 5wsc
Magnesium binding site 3 out of 4 in the Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and 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 Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg503

b:19.7
occ:1.00
 OD2 C:ASP244 1.8 31.8 1.0
O C:HOH613 2.0 23.3 1.0
OE1 C:GLU220 2.1 23.4 1.0
O C:HOH604 2.2 18.9 1.0
O1 C:OXL504 2.4 19.9 1.0
O2 C:OXL504 2.5 19.3 1.0
CG C:ASP244 2.8 27.1 1.0
CD C:GLU220 3.0 27.3 1.0
C1 C:OXL504 3.2 20.7 1.0
C2 C:OXL504 3.2 21.9 1.0
CB C:ASP244 3.4 27.3 1.0
OE2 C:GLU220 3.4 29.7 1.0
OD1 C:ASP244 3.9 24.3 1.0
NZ C:LYS218 4.1 27.8 1.0
CZ C:PHE192 4.3 30.8 1.0
N C:ASP244 4.3 26.2 1.0
CG C:GLU220 4.3 27.4 1.0
O3 C:OXL504 4.4 23.4 1.0
O4 C:OXL504 4.4 24.9 1.0
CA C:ASP244 4.5 26.0 1.0
CB C:ALA241 4.5 22.4 1.0
CE C:LYS218 4.6 25.3 1.0
CB C:GLU220 4.6 27.1 1.0
NZ C:LYS72 4.6 34.4 1.0
CE1 C:PHE192 4.6 33.6 1.0
CE2 C:PHE192 4.8 28.8 1.0
O C:ALA241 4.9 21.6 1.0

Magnesium binding site 4 out of 4 in 5wsc

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Magnesium binding site 4 out of 4 in the Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and 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 Crystal of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Soaked with Allosteric Activators Amp and Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:21.1
occ:1.00
 OD2 D:ASP244 1.8 31.7 1.0
O D:HOH602 1.9 18.9 1.0
O1 D:OXL504 2.1 22.9 1.0
OE1 D:GLU220 2.2 24.0 1.0
O D:HOH633 2.2 23.3 1.0
O4 D:OXL504 2.4 22.7 1.0
CG D:ASP244 3.0 28.2 1.0
C1 D:OXL504 3.0 22.1 1.0
CD D:GLU220 3.1 26.1 1.0
C2 D:OXL504 3.1 23.2 1.0
OE2 D:GLU220 3.4 27.9 1.0
CB D:ASP244 3.5 26.8 1.0
OD1 D:ASP244 4.0 25.2 1.0
NZ D:LYS218 4.1 28.1 1.0
CZ D:PHE192 4.1 28.8 1.0
O3 D:OXL504 4.1 22.4 1.0
O2 D:OXL504 4.3 23.7 1.0
CG D:GLU220 4.4 26.8 1.0
CE1 D:PHE192 4.5 32.1 1.0
CE2 D:PHE192 4.6 28.0 1.0
N D:ASP244 4.6 25.9 1.0
CE D:LYS218 4.6 25.9 1.0
CB D:ALA241 4.6 23.1 1.0
CB D:GLU220 4.7 27.4 1.0
CA D:ASP244 4.7 26.6 1.0
O D:HOH603 4.9 26.7 1.0
CE D:LYS72 4.9 33.8 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 Dec 14 21:24:57 2020

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