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Magnesium in PDB 6ito: Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate

Enzymatic activity of Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate

All present enzymatic activity of Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate:
2.7.1.40;

Protein crystallography data

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

Resolution Low / High (Å) 62.77 / 2.55
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 125.550, 125.550, 143.821, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 24.8

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 6ito

Go back to Magnesium Binding Sites List in 6ito
Magnesium binding site 1 out of 4 in the Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:46.0
occ:1.00
 OD2 A:ASP244 1.9 48.5 1.0
O A:HOH607 1.9 34.4 1.0
O4 A:OXL502 2.1 49.4 1.0
O3 A:OXL502 2.2 52.7 1.0
O A:HOH602 2.2 67.1 1.0
OE1 A:GLU220 2.3 47.2 1.0
C2 A:OXL502 2.9 48.1 1.0
C1 A:OXL502 2.9 48.8 1.0
CG A:ASP244 3.0 46.8 1.0
CD A:GLU220 3.2 48.3 1.0
OE2 A:GLU220 3.5 49.7 1.0
CB A:ASP244 3.7 45.5 1.0
NZ A:LYS218 3.8 42.5 1.0
OD1 A:ASP244 4.0 48.0 1.0
O A:HOH727 4.1 47.4 1.0
O2 A:OXL502 4.1 48.5 1.0
O1 A:OXL502 4.1 43.8 1.0
O A:HOH622 4.4 41.9 1.0
CE A:LYS218 4.5 41.7 1.0
CZ A:PHE192 4.6 50.2 1.0
N A:ASP244 4.6 44.9 1.0
CG A:GLU220 4.6 47.1 1.0
CB A:ALA241 4.6 41.5 1.0
CA A:ASP244 4.8 46.2 1.0
CE1 A:PHE192 4.8 49.4 1.0
CB A:GLU220 4.9 46.7 1.0

Magnesium binding site 2 out of 4 in 6ito

Go back to Magnesium Binding Sites List in 6ito
Magnesium binding site 2 out of 4 in the Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:41.3
occ:1.00
 O B:HOH603 1.9 37.0 1.0
OD2 B:ASP244 2.1 46.6 1.0
O2 B:OXL502 2.2 51.3 1.0
O B:HOH633 2.3 54.8 1.0
O1 B:OXL502 2.3 53.1 1.0
OE1 B:GLU220 2.4 44.1 1.0
C2 B:OXL502 2.9 51.2 1.0
C1 B:OXL502 3.0 49.8 1.0
CG B:ASP244 3.3 46.3 1.0
CD B:GLU220 3.3 46.5 1.0
OE2 B:GLU220 3.5 47.0 1.0
NZ B:LYS218 3.7 43.7 1.0
CB B:ASP244 3.9 46.1 1.0
O4 B:OXL502 4.2 52.5 1.0
O3 B:OXL502 4.2 42.3 1.0
OD1 B:ASP244 4.2 48.6 1.0
CE B:LYS218 4.4 42.0 1.0
O B:HOH602 4.5 45.7 1.0
CB B:ALA241 4.7 44.9 1.0
CZ B:PHE192 4.7 51.1 1.0
CG B:GLU220 4.7 45.6 1.0
N B:ASP244 4.8 44.6 1.0
NZ B:LYS72 4.8 68.8 1.0
CA B:ASP244 5.0 46.4 1.0

Magnesium binding site 3 out of 4 in 6ito

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Magnesium binding site 3 out of 4 in the Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:40.7
occ:1.00
 OD2 C:ASP244 2.0 50.2 1.0
O C:HOH612 2.0 60.2 1.0
O C:HOH607 2.0 37.9 1.0
O3 C:OXL502 2.2 54.2 1.0
O4 C:OXL502 2.3 56.4 1.0
OE1 C:GLU220 2.4 47.9 1.0
C1 C:OXL502 2.9 51.6 1.0
C2 C:OXL502 3.0 53.1 1.0
CG C:ASP244 3.1 49.6 1.0
CD C:GLU220 3.4 48.6 1.0
OE2 C:GLU220 3.6 51.1 1.0
O C:HOH699 3.7 40.4 1.0
NZ C:LYS218 3.8 48.2 1.0
CB C:ASP244 3.9 47.8 1.0
O1 C:OXL502 4.1 42.6 1.0
OD1 C:ASP244 4.1 50.5 1.0
O2 C:OXL502 4.2 52.2 1.0
O C:HOH695 4.3 35.7 1.0
O C:HOH608 4.4 51.6 1.0
CE C:LYS218 4.6 46.8 1.0
CZ C:PHE192 4.7 52.9 1.0
N C:ASP244 4.7 45.3 1.0
CB C:ALA241 4.7 42.4 1.0
CG C:GLU220 4.8 46.6 1.0
CA C:ASP244 4.9 48.0 1.0
CE1 C:PHE192 5.0 51.6 1.0

Magnesium binding site 4 out of 4 in 6ito

Go back to Magnesium Binding Sites List in 6ito
Magnesium binding site 4 out of 4 in the Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, Amp and Inhibitor Ribose 5- Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:46.5
occ:1.00
 O D:HOH607 1.8 28.9 1.0
O D:HOH602 2.0 50.1 1.0
OD2 D:ASP244 2.0 45.0 1.0
O1 D:OXL502 2.1 51.4 1.0
OE1 D:GLU220 2.1 50.2 1.0
O2 D:OXL502 2.3 50.8 1.0
C1 D:OXL502 2.9 50.3 1.0
C2 D:OXL502 3.0 51.1 1.0
CD D:GLU220 3.1 50.1 1.0
CG D:ASP244 3.2 45.1 1.0
OE2 D:GLU220 3.4 51.7 1.0
NZ D:LYS218 3.7 45.0 1.0
CB D:ASP244 3.8 44.7 1.0
O3 D:OXL502 4.1 44.6 1.0
O D:HOH694 4.1 45.5 1.0
OD1 D:ASP244 4.2 46.0 1.0
O4 D:OXL502 4.2 53.3 1.0
O D:HOH603 4.4 50.8 1.0
CE D:LYS218 4.4 43.6 1.0
CB D:ALA241 4.5 44.5 1.0
CG D:GLU220 4.5 48.5 1.0
N D:ASP244 4.6 44.2 1.0
O D:HOH646 4.7 42.0 1.0
CZ D:PHE192 4.7 52.8 1.0
CA D:ASP244 4.8 45.3 1.0
CB D:GLU220 4.8 47.6 1.0
CE1 D:PHE192 4.9 51.8 1.0

Reference:

W.Zhong, J.Guo, L.Cui, Y.H.Chionh, K.Li, A.El Sahili, Q.Cai, M.Yuan, P.A.M.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw, Y.Mu, J.Lescar, P.C.Dedon. Pyruvate Kinase Regulates the Pentose-Phosphate Pathway in Response to Hypoxia in Mycobacterium Tuberculosis. J.Mol.Biol. V. 431 3690 2019.
ISSN: ESSN 1089-8638
PubMed: 31381898
DOI: 10.1016/J.JMB.2019.07.033
Page generated: Wed Aug 13 08:49:51 2025

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