Atomistry » Magnesium » PDB 5wi5-5wti » 5wsb
Atomistry »
  Magnesium »
    PDB 5wi5-5wti »
      5wsb »

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

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

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

Protein crystallography data

The structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate, PDB code: 5wsb 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) 62.82 / 2.25
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 125.631, 125.631, 144.514, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 22.8

Other elements in 5wsb:

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

Magnesium binding site 1 out of 4 in 5wsb

Go back to Magnesium Binding Sites List in 5wsb
Magnesium binding site 1 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, 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 Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:32.9
occ:1.00
 O A:HOH633 2.0 23.8 1.0
O A:HOH636 2.0 30.8 1.0
O4 A:OXL504 2.1 30.0 1.0
OD2 A:ASP244 2.1 34.0 1.0
OE1 A:GLU220 2.1 29.8 1.0
O3 A:OXL504 2.2 23.1 1.0
C2 A:OXL504 2.9 29.3 1.0
C1 A:OXL504 2.9 31.1 1.0
CD A:GLU220 3.1 32.9 1.0
CG A:ASP244 3.2 31.9 1.0
OE2 A:GLU220 3.4 28.4 1.0
NZ A:LYS218 3.7 31.3 1.0
CB A:ASP244 3.8 30.5 1.0
O2 A:OXL504 4.1 25.2 1.0
O1 A:OXL504 4.2 23.6 1.0
OD1 A:ASP244 4.2 31.3 1.0
CE A:LYS218 4.3 32.0 1.0
CG A:GLU220 4.5 33.5 1.0
CZ A:PHE192 4.5 32.9 1.0
N A:ASP244 4.6 32.4 1.0
CB A:ALA241 4.6 31.6 1.0
OG A:SER191 4.7 32.8 1.0
CE1 A:PHE192 4.8 31.5 1.0
CB A:GLU220 4.8 34.6 1.0
CA A:ASP244 4.9 33.0 1.0
CE2 A:PHE192 5.0 32.4 1.0

Magnesium binding site 2 out of 4 in 5wsb

Go back to Magnesium Binding Sites List in 5wsb
Magnesium binding site 2 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, 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 Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Allosteric Activators Amp and Glucose 6-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:35.2
occ:1.00
 O2 B:OXL504 2.0 26.5 1.0
OD2 B:ASP244 2.0 37.6 1.0
O B:HOH625 2.1 27.3 1.0
O1 B:OXL504 2.2 22.0 1.0
O B:HOH660 2.2 21.7 1.0
OE1 B:GLU220 2.3 33.2 1.0
C2 B:OXL504 2.7 32.0 1.0
C1 B:OXL504 2.8 30.1 1.0
CG B:ASP244 3.2 33.9 1.0
CD B:GLU220 3.3 35.4 1.0
OE2 B:GLU220 3.5 34.2 1.0
CB B:ASP244 3.8 31.4 1.0
NZ B:LYS218 3.9 30.5 1.0
O4 B:OXL504 4.0 29.9 1.0
O3 B:OXL504 4.0 25.2 1.0
OD1 B:ASP244 4.2 35.9 1.0
O B:HOH642 4.3 19.2 1.0
CZ B:PHE192 4.3 31.8 1.0
CE B:LYS218 4.6 31.0 1.0
N B:ASP244 4.7 32.4 1.0
CG B:GLU220 4.7 34.3 1.0
CE1 B:PHE192 4.7 30.7 1.0
CE2 B:PHE192 4.8 32.5 1.0
OG B:SER191 4.8 31.6 1.0
CA B:ASP244 4.9 33.2 1.0
CB B:ALA241 5.0 31.7 1.0

Magnesium binding site 3 out of 4 in 5wsb

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

b:32.3
occ:1.00
 OD2 C:ASP244 1.9 39.1 1.0
O C:HOH630 1.9 28.2 1.0
O C:HOH606 2.0 27.2 1.0
OE1 C:GLU220 2.2 33.0 1.0
O2 C:OXL504 2.3 29.3 1.0
O1 C:OXL504 2.5 29.7 1.0
CG C:ASP244 3.0 36.4 1.0
C2 C:OXL504 3.1 27.9 1.0
C1 C:OXL504 3.1 29.9 1.0
CD C:GLU220 3.2 32.1 1.0
OE2 C:GLU220 3.5 29.6 1.0
CB C:ASP244 3.6 36.6 1.0
OD1 C:ASP244 4.0 32.8 1.0
NZ C:LYS218 4.1 31.5 1.0
O4 C:OXL504 4.2 24.3 1.0
N C:ASP244 4.3 36.8 1.0
O3 C:OXL504 4.3 26.1 1.0
NZ C:LYS72 4.4 52.4 1.0
CZ C:PHE192 4.4 38.3 1.0
CG C:GLU220 4.6 32.1 1.0
CE C:LYS218 4.6 32.2 1.0
CA C:ASP244 4.6 35.4 1.0
CB C:ALA241 4.6 29.3 1.0
CE1 C:PHE192 4.7 38.2 1.0
CB C:GLU220 4.8 34.4 1.0
CE2 C:PHE192 4.9 40.5 1.0
OG C:SER191 5.0 31.1 1.0

Magnesium binding site 4 out of 4 in 5wsb

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

b:30.8
occ:1.00
 OD2 D:ASP244 1.8 39.6 1.0
O1 D:OXL504 1.9 26.9 1.0
OE1 D:GLU220 1.9 34.0 1.0
O D:HOH652 2.2 23.8 1.0
O D:HOH640 2.3 23.6 1.0
O2 D:OXL504 2.5 29.9 1.0
C1 D:OXL504 2.8 29.1 1.0
CG D:ASP244 2.9 37.0 1.0
CD D:GLU220 3.0 33.1 1.0
C2 D:OXL504 3.1 30.0 1.0
CB D:ASP244 3.4 37.3 1.0
OE2 D:GLU220 3.5 31.5 1.0
OD1 D:ASP244 4.0 37.3 1.0
O3 D:OXL504 4.0 24.9 1.0
N D:ASP244 4.1 38.5 1.0
CG D:GLU220 4.3 34.0 1.0
O4 D:OXL504 4.3 29.2 1.0
CA D:ASP244 4.4 37.6 1.0
NZ D:LYS218 4.4 29.2 1.0
CZ D:PHE192 4.4 39.4 1.0
CB D:ALA241 4.5 29.5 1.0
CB D:GLU220 4.5 34.0 1.0
CE1 D:PHE192 4.6 39.5 1.0
CE D:LYS218 4.8 29.6 1.0
O D:HOH649 4.8 34.3 1.0
O D:HOH637 4.9 26.2 1.0
CE2 D:PHE192 4.9 41.3 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 08:22:19 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy