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Magnesium in PDB 5ws9: Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp

Enzymatic activity of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp

All present enzymatic activity of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp:
2.7.1.40;

Protein crystallography data

The structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp, PDB code: 5ws9 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) 60.54 / 1.90
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 127.190, 127.190, 144.924, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 22.3

Other elements in 5ws9:

The structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp also contains other interesting chemical elements:

Potassium (K) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp (pdb code 5ws9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp, PDB code: 5ws9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5ws9

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Magnesium binding site 1 out of 6 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp


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, Atp and Allosteric Activator Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:28.8
occ:1.00
 OD2 A:ASP244 2.0 26.6 1.0
OE1 A:GLU220 2.1 24.3 1.0
O1 A:OXL502 2.1 27.7 1.0
O2 A:OXL502 2.2 31.0 1.0
O A:HOH709 2.2 27.6 1.0
O A:HOH784 2.2 23.6 1.0
C1 A:OXL502 2.9 30.7 1.0
C2 A:OXL502 2.9 35.9 1.0
CG A:ASP244 3.1 31.1 1.0
CD A:GLU220 3.1 24.7 1.0
OE2 A:GLU220 3.5 22.7 1.0
CB A:ASP244 3.5 27.3 1.0
O A:HOH717 3.9 46.7 1.0
O3 A:OXL502 4.1 28.3 1.0
O4 A:OXL502 4.1 35.4 1.0
OD1 A:ASP244 4.2 31.0 1.0
NZ A:LYS218 4.2 25.0 1.0
N A:ASP244 4.3 26.2 1.0
CZ A:PHE192 4.4 27.1 1.0
O A:HOH786 4.4 38.2 1.0
CG A:GLU220 4.5 25.2 1.0
CE A:LYS218 4.5 25.4 1.0
CB A:ALA241 4.5 24.9 1.0
CA A:ASP244 4.5 26.1 1.0
CE1 A:PHE192 4.6 27.7 1.0
O A:HOH643 4.6 27.3 1.0
CB A:GLU220 4.7 26.1 1.0
O A:HOH613 5.0 58.2 1.0
CE2 A:PHE192 5.0 27.8 1.0

Magnesium binding site 2 out of 6 in 5ws9

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Magnesium binding site 2 out of 6 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp


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, Atp and Allosteric Activator Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:30.4
occ:1.00
 OD2 B:ASP244 1.9 26.4 1.0
OE1 B:GLU220 2.1 26.2 1.0
O3 B:OXL502 2.2 30.2 1.0
O B:HOH702 2.2 27.5 1.0
O B:HOH796 2.2 24.4 1.0
O4 B:OXL502 2.2 30.2 1.0
C1 B:OXL502 2.9 32.7 1.0
C2 B:OXL502 2.9 36.6 1.0
CG B:ASP244 3.0 30.3 1.0
CD B:GLU220 3.1 26.1 1.0
OE2 B:GLU220 3.5 23.8 1.0
CB B:ASP244 3.5 27.4 1.0
O B:HOH688 3.7 45.7 1.0
OD1 B:ASP244 4.1 28.5 1.0
O1 B:OXL502 4.1 29.3 1.0
O2 B:OXL502 4.2 39.0 1.0
NZ B:LYS218 4.2 24.1 1.0
CZ B:PHE192 4.3 27.8 1.0
N B:ASP244 4.3 26.8 1.0
O B:HOH862 4.3 34.5 1.0
CE B:LYS218 4.5 24.6 1.0
CG B:GLU220 4.5 26.0 1.0
CE1 B:PHE192 4.5 27.2 1.0
CA B:ASP244 4.6 27.2 1.0
O B:HOH689 4.6 25.5 1.0
CB B:ALA241 4.6 26.1 1.0
CB B:GLU220 4.7 27.7 1.0
CE2 B:PHE192 4.9 27.3 1.0

Magnesium binding site 3 out of 6 in 5ws9

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Magnesium binding site 3 out of 6 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp


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, Atp and Allosteric Activator Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:30.4
occ:1.00
 OD2 C:ASP244 1.9 35.4 1.0
OE1 C:GLU220 2.0 30.2 1.0
O C:HOH635 2.1 28.0 1.0
O C:HOH680 2.1 31.2 1.0
O1 C:OXL503 2.2 28.6 1.0
O4 C:OXL503 2.4 35.3 1.0
CG C:ASP244 3.0 31.7 1.0
CD C:GLU220 3.0 32.2 1.0
C1 C:OXL503 3.1 35.2 1.0
C2 C:OXL503 3.1 37.1 1.0
OE2 C:GLU220 3.4 30.2 1.0
CB C:ASP244 3.5 31.1 1.0
OD1 C:ASP244 4.0 34.6 1.0
CZ C:PHE192 4.1 38.9 1.0
O3 C:OXL503 4.3 34.3 1.0
NZ C:LYS218 4.3 33.5 1.0
O2 C:OXL503 4.3 39.7 1.0
CG C:GLU220 4.4 31.8 1.0
O C:HOH713 4.4 49.5 1.0
N C:ASP244 4.4 31.1 1.0
CE1 C:PHE192 4.4 38.1 1.0
O C:HOH748 4.4 31.6 1.0
CE C:LYS218 4.5 31.0 1.0
CB C:ALA241 4.6 28.5 1.0
CA C:ASP244 4.6 29.8 1.0
CB C:GLU220 4.6 31.5 1.0
CE2 C:PHE192 4.7 39.3 1.0

Magnesium binding site 4 out of 6 in 5ws9

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Magnesium binding site 4 out of 6 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp


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, Atp and Allosteric Activator Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:71.6
occ:1.00
 O2A C:ATP505 2.4 51.1 0.9
O C:HOH649 2.5 54.3 1.0
O2G C:ATP505 2.8 59.0 0.9
O2B C:ATP505 2.8 53.4 0.9
O C:HOH854 3.2 44.5 1.0
PA C:ATP505 3.6 59.2 0.9
PB C:ATP505 3.8 58.4 0.9
OD2 C:ASP126 4.0 61.3 1.0
CG2 C:THR276 4.0 35.9 1.0
O3A C:ATP505 4.0 61.2 0.9
PG C:ATP505 4.1 66.0 0.9
O C:HOH680 4.1 31.2 1.0
O3 C:OXL503 4.1 34.3 1.0
O1A C:ATP505 4.2 44.4 0.9
C1 C:OXL503 4.2 35.2 1.0
O3B C:ATP505 4.4 66.2 0.9
OG1 C:THR276 4.5 34.0 1.0
C2 C:OXL503 4.5 37.1 1.0
O1 C:OXL503 4.5 28.6 1.0
O1G C:ATP505 4.7 51.1 0.9
O2 C:OXL503 4.7 39.7 1.0
O C:HOH713 4.9 49.5 1.0
CB C:THR276 4.9 30.7 1.0
CG C:ASP126 4.9 57.1 1.0
O5' C:ATP505 5.0 58.5 0.9

Magnesium binding site 5 out of 6 in 5ws9

Go back to Magnesium Binding Sites List in 5ws9
Magnesium binding site 5 out of 6 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:33.2
occ:1.00
 OD2 D:ASP244 1.9 33.6 1.0
OE1 D:GLU220 2.0 31.5 1.0
O D:HOH638 2.1 28.6 1.0
O D:HOH666 2.2 27.6 1.0
O3 D:OXL503 2.2 31.2 1.0
O2 D:OXL503 2.4 40.0 1.0
CG D:ASP244 3.0 32.7 1.0
CD D:GLU220 3.0 32.4 1.0
C1 D:OXL503 3.0 38.0 1.0
C2 D:OXL503 3.1 38.5 1.0
OE2 D:GLU220 3.4 30.6 1.0
CB D:ASP244 3.5 31.2 1.0
O D:HOH692 3.8 42.9 1.0
OD1 D:ASP244 4.0 34.0 1.0
CZ D:PHE192 4.1 40.9 1.0
O1 D:OXL503 4.2 34.4 1.0
NZ D:LYS218 4.2 29.6 1.0
O D:HOH741 4.3 27.8 1.0
O4 D:OXL503 4.4 40.6 1.0
CG D:GLU220 4.4 31.7 1.0
N D:ASP244 4.4 30.8 1.0
CE1 D:PHE192 4.4 39.8 1.0
O D:HOH731 4.4 50.1 1.0
CE D:LYS218 4.5 29.5 1.0
CA D:ASP244 4.6 30.7 1.0
CB D:ALA241 4.6 30.5 1.0
CB D:GLU220 4.6 31.8 1.0
CE2 D:PHE192 4.7 40.9 1.0

Magnesium binding site 6 out of 6 in 5ws9

Go back to Magnesium Binding Sites List in 5ws9
Magnesium binding site 6 out of 6 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp


Mono view


Stereo pair view

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

b:69.0
occ:1.00
 O1A D:ATP506 2.2 42.6 0.9
O D:HOH626 2.4 51.3 1.0
O1G D:ATP506 2.7 50.9 0.9
O1B D:ATP506 2.9 64.5 0.9
O D:HOH857 3.0 44.5 1.0
O D:HOH692 3.1 42.9 1.0
PA D:ATP506 3.4 54.7 0.9
OD2 D:ASP126 3.9 66.4 1.0
O D:HOH637 3.9 46.3 1.0
O2A D:ATP506 3.9 41.5 0.9
PB D:ATP506 3.9 60.5 0.9
O3A D:ATP506 4.0 57.5 0.9
PG D:ATP506 4.1 62.0 0.9
CG2 D:THR276 4.1 33.4 1.0
O D:HOH666 4.2 27.6 1.0
O3B D:ATP506 4.4 58.8 0.9
C1 D:OXL503 4.5 38.0 1.0
O1 D:OXL503 4.6 34.4 1.0
O D:HOH847 4.7 44.0 1.0
OG1 D:THR276 4.7 33.9 1.0
O3 D:OXL503 4.8 31.2 1.0
O5' D:ATP506 4.8 57.0 0.9
C2 D:OXL503 4.8 38.5 1.0
CG D:ASP126 4.9 62.0 1.0
O3G D:ATP506 4.9 46.8 0.9

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 08:16:20 2024

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