Magnesium in PDB 5ws8: Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate

All present enzymatic activity of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate:
2.7.1.40;

The structure of Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate, PDB code: 5ws8 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)	63.51 / 2.62
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	127.011, 127.011, 144.652, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 21.8

The binding sites of Magnesium atom in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate (pdb code 5ws8). 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, PDB code: 5ws8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:53.2 occ:1.00 OD2 A:ASP244 2.0 59.1 1.0 O A:HOH612 2.0 47.6 1.0 OE1 A:GLU220 2.1 47.9 1.0 O2 A:OXL502 2.2 72.0 1.0 O A:HOH637 2.2 39.9 1.0 O1 A:OXL502 2.2 58.8 1.0 C2 A:OXL502 3.0 74.7 1.0 C1 A:OXL502 3.0 62.9 1.0 CD A:GLU220 3.0 53.6 1.0 CG A:ASP244 3.1 58.7 1.0 OE2 A:GLU220 3.3 56.3 1.0 NZ A:LYS218 3.7 55.1 1.0 CB A:ASP244 3.9 55.6 1.0 O A:HOH678 4.0 56.0 1.0 OD1 A:ASP244 4.1 61.0 1.0 O A:HOH605 4.1 63.9 1.0 O3 A:OXL502 4.2 53.4 1.0 O4 A:OXL502 4.2 78.5 1.0 CZ A:PHE192 4.3 56.5 1.0 CG A:GLU220 4.5 52.9 1.0 CE A:LYS218 4.5 51.3 1.0 NZ A:LYS72 4.5 79.0 1.0 O A:HOH613 4.5 52.0 1.0 CB A:ALA241 4.6 50.8 1.0 CE1 A:PHE192 4.6 56.6 1.0 N A:ASP244 4.7 52.9 1.0 CE2 A:PHE192 4.8 57.2 1.0 CB A:GLU220 4.9 54.3 1.0 CA A:ASP244 5.0 54.3 1.0

Magnesium binding site 2 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:53.3 occ:1.00 O B:HOH610 1.9 55.6 1.0 OD2 B:ASP244 2.0 53.0 1.0 O B:HOH639 2.1 44.3 1.0 O4 B:OXL502 2.1 73.5 1.0 OE1 B:GLU220 2.2 47.4 1.0 O3 B:OXL502 2.3 58.6 1.0 C2 B:OXL502 2.9 72.3 1.0 C1 B:OXL502 3.0 61.1 1.0 CD B:GLU220 3.1 56.1 1.0 CG B:ASP244 3.2 55.3 1.0 OE2 B:GLU220 3.3 58.2 1.0 NZ B:LYS218 3.6 56.1 1.0 CB B:ASP244 4.0 53.5 1.0 O B:HOH617 4.1 64.2 1.0 OD1 B:ASP244 4.1 58.5 1.0 O2 B:OXL502 4.1 80.3 1.0 O1 B:OXL502 4.2 56.4 1.0 CZ B:PHE192 4.3 54.5 1.0 NZ B:LYS72 4.4 83.7 1.0 CE B:LYS218 4.5 53.8 1.0 CG B:GLU220 4.6 55.9 1.0 CB B:ALA241 4.6 52.2 1.0 CE1 B:PHE192 4.7 54.3 1.0 N B:ASP244 4.8 51.1 1.0 CE2 B:PHE192 4.8 54.8 1.0 OG B:SER191 5.0 58.1 1.0

Magnesium binding site 3 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:55.1 occ:1.00 O C:HOH603 2.0 52.9 1.0 O2 C:OXL502 2.0 78.7 1.0 OD2 C:ASP244 2.0 55.1 1.0 O C:HOH674 2.2 53.4 1.0 O1 C:OXL502 2.2 58.4 1.0 OE1 C:GLU220 2.5 45.9 1.0 C2 C:OXL502 2.8 72.6 1.0 C1 C:OXL502 2.9 60.5 1.0 CG C:ASP244 3.2 53.6 1.0 CD C:GLU220 3.4 57.0 1.0 OE2 C:GLU220 3.6 59.7 1.0 NZ C:LYS218 3.7 56.0 1.0 O4 C:OXL502 4.0 79.4 1.0 OD1 C:ASP244 4.1 54.7 1.0 CB C:ASP244 4.1 53.7 1.0 O3 C:OXL502 4.1 53.0 1.0 NZ C:LYS72 4.3 79.3 1.0 O C:HOH610 4.4 60.5 1.0 CZ C:PHE192 4.5 55.1 1.0 CE C:LYS218 4.6 55.4 1.0 N C:ASP244 4.7 49.5 1.0 CG C:GLU220 4.8 57.3 1.0 CB C:ALA241 4.9 47.6 1.0 CE1 C:PHE192 4.9 55.6 1.0 CE2 C:PHE192 4.9 56.6 1.0

Magnesium binding site 4 out of 4 in the Pyruvate Kinase (Pyk) From Mycobacterium Tuberculosis in Complex with Oxalate


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:53.2 occ:1.00 O D:HOH607 1.9 63.9 1.0 OD2 D:ASP244 2.1 58.1 1.0 O3 D:OXL502 2.1 57.7 1.0 OE1 D:GLU220 2.1 48.4 1.0 O D:HOH647 2.2 50.4 1.0 O4 D:OXL502 2.3 83.2 1.0 C1 D:OXL502 2.9 64.8 1.0 C2 D:OXL502 3.0 77.8 1.0 CD D:GLU220 3.1 58.4 1.0 CG D:ASP244 3.3 57.1 1.0 OE2 D:GLU220 3.3 61.1 1.0 NZ D:LYS218 3.6 57.8 1.0 CB D:ASP244 4.0 54.8 1.0 O1 D:OXL502 4.1 54.8 1.0 OD1 D:ASP244 4.1 60.4 1.0 O2 D:OXL502 4.3 87.0 1.0 CZ D:PHE192 4.4 52.1 1.0 CE D:LYS218 4.4 54.4 1.0 CG D:GLU220 4.5 56.5 1.0 NZ D:LYS72 4.5 80.3 1.0 CB D:ALA241 4.6 51.0 1.0 N D:ASP244 4.7 51.2 1.0 CE1 D:PHE192 4.8 51.2 1.0 CE2 D:PHE192 4.9 52.0 1.0 CB D:GLU220 5.0 55.7 1.0 OG D:SER191 5.0 53.4 1.0

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