Magnesium in PDB 7yh5: Mazg(Mycobacterium Tuberculosis)

All present enzymatic activity of Mazg(Mycobacterium Tuberculosis):
3.6.1.19; 3.6.1.8;

The structure of Mazg(Mycobacterium Tuberculosis), PDB code: 7yh5 was solved by J.Li, S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.86 / 2.70
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.31, 109.31, 242.91, 90, 90, 90
R / Rfree (%)	25.8 / 29.6

The binding sites of Magnesium atom in the Mazg(Mycobacterium Tuberculosis) (pdb code 7yh5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Mazg(Mycobacterium Tuberculosis), PDB code: 7yh5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Mazg(Mycobacterium Tuberculosis)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mazg(Mycobacterium Tuberculosis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:83.6 occ:1.00 OE1 A:GLU119 2.1 86.2 1.0 OE2 A:GLU122 2.3 87.0 1.0 OE1 A:GLU138 2.6 92.5 1.0 OD2 A:ASP141 2.6 97.3 1.0 OE2 A:GLU138 2.6 92.2 1.0 CD A:GLU119 2.9 91.8 1.0 CD A:GLU138 3.0 88.4 1.0 OE2 A:GLU119 3.0 90.9 1.0 CD A:GLU122 3.5 82.3 1.0 O A:HOH301 3.5 80.4 1.0 CG A:ASP141 3.6 93.4 1.0 CB A:ASP141 4.1 86.2 1.0 OE1 A:GLU122 4.2 89.1 1.0 CG A:GLU119 4.4 87.9 1.0 CB A:GLU122 4.4 77.3 1.0 CG A:GLU138 4.5 86.1 1.0 CG A:GLU122 4.5 81.8 1.0 OD1 A:ASP141 4.6 90.1 1.0 CB A:GLU119 4.8 83.4 1.0 CA A:GLU119 5.0 81.8 1.0

Magnesium binding site 2 out of 6 in the Mazg(Mycobacterium Tuberculosis)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mazg(Mycobacterium Tuberculosis) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:85.5 occ:1.00 OE1 B:GLU138 2.2 90.6 1.0 OE2 B:GLU119 2.2 88.7 1.0 OD2 B:ASP141 2.3 105.6 1.0 OE2 B:GLU122 2.8 100.5 1.0 CD B:GLU138 2.9 96.9 1.0 OE2 B:GLU138 3.0 100.4 1.0 CD B:GLU119 3.1 90.6 1.0 CD B:GLU122 3.2 94.0 1.0 OE1 B:GLU122 3.3 97.5 1.0 OE1 B:GLU119 3.3 94.0 1.0 CG B:ASP141 3.5 103.3 1.0 CB B:ASP141 4.2 88.9 1.0 CB B:GLU122 4.3 86.7 1.0 CG B:GLU122 4.3 94.2 1.0 CG B:GLU138 4.4 90.9 1.0 OD1 B:ASP141 4.5 98.3 1.0 CG B:GLU119 4.5 91.3 1.0

Magnesium binding site 3 out of 6 in the Mazg(Mycobacterium Tuberculosis)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mazg(Mycobacterium Tuberculosis) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:77.5 occ:1.00 OE2 C:GLU122 2.0 101.1 1.0 OE1 C:GLU138 2.8 91.7 1.0 OE2 C:GLU138 2.8 81.5 1.0 CD C:GLU122 3.0 92.7 1.0 CD C:GLU138 3.2 91.1 1.0 OD2 C:ASP141 3.5 96.8 1.0 OE1 C:GLU119 3.5 93.4 1.0 OE1 C:GLU122 3.5 98.1 1.0 OE2 C:GLU119 3.6 97.7 1.0 CD C:GLU119 4.0 92.9 1.0 CG C:GLU122 4.2 88.6 1.0 CB C:GLU122 4.3 85.5 1.0 CG C:ASP141 4.5 91.2 1.0 OE2 C:GLU137 4.6 112.6 1.0 NZ D:LYS173 4.6 91.2 1.0 CG C:GLU138 4.6 91.4 1.0

Magnesium binding site 4 out of 6 in the Mazg(Mycobacterium Tuberculosis)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mazg(Mycobacterium Tuberculosis) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:80.6 occ:1.00 OE1 D:GLU122 2.5 99.6 1.0 OD2 D:ASP141 3.2 86.8 1.0 OE2 D:GLU138 3.3 88.2 1.0 CD D:GLU122 3.4 95.2 1.0 OE1 D:GLU119 3.5 88.2 1.0 OE2 D:GLU122 3.5 96.0 1.0 OE1 D:GLU138 3.8 87.4 1.0 OE2 D:GLU119 3.9 86.7 1.0 CD D:GLU138 4.0 91.3 1.0 CD D:GLU119 4.1 84.0 1.0 CG D:ASP141 4.2 89.3 1.0 NZ C:LYS173 4.3 88.1 1.0 OE1 D:GLU137 4.6 100.3 1.0 OE2 D:GLU118 4.7 106.6 1.0 CG D:GLU122 4.8 85.4 1.0 OD1 D:ASP141 4.9 88.8 1.0

Magnesium binding site 5 out of 6 in the Mazg(Mycobacterium Tuberculosis)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mazg(Mycobacterium Tuberculosis) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:94.1 occ:1.00 OE1 E:GLU119 2.7 106.4 1.0 OE2 E:GLU119 3.3 101.0 1.0 CD E:GLU119 3.3 106.1 1.0 CB E:GLU122 3.5 96.2 1.0 CB E:GLU138 3.8 103.7 1.0 CA E:GLU138 3.9 108.3 1.0 N E:GLU138 4.4 109.4 1.0 CB E:ASP141 4.6 109.1 1.0 CG E:GLU119 4.8 104.3 1.0 CA E:GLU122 4.8 104.3 1.0 C E:GLU137 4.9 108.2 1.0

Magnesium binding site 6 out of 6 in the Mazg(Mycobacterium Tuberculosis)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mazg(Mycobacterium Tuberculosis) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:97.0 occ:1.00 OE2 F:GLU122 2.2 110.1 1.0 OE1 F:GLU138 2.2 102.0 1.0 OE2 F:GLU138 2.7 108.9 1.0 CD F:GLU138 2.8 105.3 1.0 CD F:GLU122 3.0 110.2 1.0 OE2 F:GLU119 3.1 104.1 1.0 OE1 F:GLU119 3.1 104.6 1.0 OE1 F:GLU122 3.4 110.8 1.0 CD F:GLU119 3.4 108.1 1.0 CG F:ASP141 3.6 115.0 1.0 OD2 F:ASP141 3.7 115.2 1.0 OD1 F:ASP141 3.9 120.3 1.0 CB F:ASP141 4.1 109.7 1.0 CG F:GLU122 4.3 99.8 1.0 CG F:GLU138 4.3 100.4 1.0 CB F:GLU122 4.4 96.5 1.0 CG F:GLU119 4.9 106.5 1.0 CB F:GLU138 4.9 107.6 1.0

S.Wang, B.Gao, A.Chen, Z.Zhang, S.Wang, L.Lv, G.Zhao, J.Li. Structural Analysis of the Housecleaning Nucleoside Triphosphate Pyrophosphohydrolase Mazg From Mycobacterium Tuberculosis. Front Microbiol V. 14 37279 2023.
ISSN: ESSN 1664-302X
PubMed: 36937295
DOI: 10.3389/FMICB.2023.1137279