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Potassium 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:

Magnesium (Mg) 6 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 3 binding sites of Potassium where determined in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Atp and Allosteric Activator Amp, PDB code: 5ws9:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 5ws9

Go back to Potassium Binding Sites List in 5ws9
Potassium binding site 1 out of 3 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 Potassium with other atoms in the K 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:K504

b:58.4
occ:1.00
 OD1 A:ASP67 2.9 28.5 1.0
OD1 A:ASN35 3.0 29.5 1.0
O A:HOH786 3.1 38.2 1.0
OG A:SER37 3.2 33.4 1.0
O A:HOH643 3.3 27.3 1.0
OG A:SER191 3.5 22.9 1.0
CG A:ASP67 3.5 29.7 1.0
NZ A:LYS218 3.7 25.0 1.0
CA A:GLN69 3.8 25.9 1.0
OD2 A:ASP67 3.9 30.1 1.0
CG A:ASN35 3.9 29.5 1.0
O A:LEU68 3.9 25.6 1.0
NH2 A:ARG33 4.0 32.2 1.0
N A:GLN69 4.1 25.6 1.0
C A:LEU68 4.2 25.2 1.0
ND2 A:ASN35 4.3 30.1 1.0
CB A:SER37 4.3 31.8 1.0
O A:ASP67 4.3 26.3 1.0
O A:HOH709 4.4 27.6 1.0
CB A:GLN69 4.6 26.5 1.0
CB A:ASP67 4.6 27.1 1.0
O A:GLN69 4.6 25.9 1.0
C A:GLN69 4.6 26.6 1.0
C A:ASP67 4.6 26.0 1.0
O1G A:ATP505 4.6 48.8 0.8
N A:SER37 4.7 28.1 1.0
CB A:SER191 4.7 25.2 1.0
O A:HOH784 4.9 23.6 1.0

Potassium binding site 2 out of 3 in 5ws9

Go back to Potassium Binding Sites List in 5ws9
Potassium binding site 2 out of 3 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 Potassium with other atoms in the K 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:K504

b:59.6
occ:1.00
 OD1 B:ASP67 2.9 27.5 1.0
O B:HOH689 2.9 25.5 1.0
O B:HOH862 3.0 34.5 1.0
OD1 B:ASN35 3.1 29.5 1.0
OG B:SER37 3.3 32.9 1.0
OG B:SER191 3.3 24.2 1.0
NZ B:LYS218 3.6 24.1 1.0
CG B:ASP67 3.6 29.5 1.0
CA B:GLN69 3.7 25.1 1.0
O B:LEU68 3.9 25.4 1.0
OD2 B:ASP67 3.9 30.5 1.0
CG B:ASN35 4.1 30.5 1.0
NH2 B:ARG33 4.1 31.5 1.0
N B:GLN69 4.1 24.8 1.0
C B:LEU68 4.1 25.8 1.0
O B:HOH702 4.2 27.5 1.0
CB B:SER37 4.4 30.2 1.0
O B:ASP67 4.4 24.1 1.0
ND2 B:ASN35 4.5 30.8 1.0
O B:GLN69 4.5 25.3 1.0
C B:GLN69 4.5 26.5 1.0
CB B:SER191 4.6 24.7 1.0
CB B:GLN69 4.6 26.6 1.0
CB B:ASP67 4.7 26.9 1.0
C B:ASP67 4.7 26.1 1.0
O2G B:ATP505 4.8 46.0 0.8
O B:HOH796 4.8 24.4 1.0
N B:SER37 4.8 29.4 1.0

Potassium binding site 3 out of 3 in 5ws9

Go back to Potassium Binding Sites List in 5ws9
Potassium binding site 3 out of 3 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 Potassium with other atoms in the K 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
D:K505

b:66.2
occ:1.00
 OD1 D:ASP67 2.9 33.9 1.0
O D:HOH731 3.0 50.1 1.0
OD1 D:ASN35 3.0 34.6 1.0
O D:HOH741 3.1 27.8 1.0
OG D:SER37 3.2 42.0 1.0
OG D:SER191 3.4 33.1 1.0
CG D:ASP67 3.5 34.3 1.0
NZ D:LYS218 3.6 29.6 1.0
CA D:GLN69 3.7 35.8 1.0
OD2 D:ASP67 3.8 35.0 1.0
O D:LEU68 3.9 34.1 1.0
CG D:ASN35 3.9 35.9 1.0
C D:LEU68 4.2 36.1 1.0
N D:GLN69 4.2 35.8 1.0
NH2 D:ARG33 4.2 40.1 1.0
ND2 D:ASN35 4.3 35.4 1.0
O D:HOH638 4.4 28.6 1.0
O3G D:ATP506 4.4 46.8 0.9
O D:ASP67 4.4 33.8 1.0
CB D:SER37 4.4 40.9 1.0
O D:GLN69 4.5 36.1 1.0
CB D:ASP67 4.5 32.6 1.0
C D:GLN69 4.5 37.0 1.0
CB D:GLN69 4.6 38.2 1.0
CB D:SER191 4.6 33.1 1.0
C D:ASP67 4.7 33.4 1.0
N D:SER37 4.8 40.5 1.0
O D:HOH666 4.9 27.6 1.0
CG D:GLN69 5.0 39.9 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 00:12:17 2020

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