Magnesium in PDB 7whs: Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp

The binding sites of Magnesium atom in the Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp (pdb code 7whs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp, PDB code: 7whs:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:50.9 occ:1.00 OD1 A:ASP226 2.3 52.0 1.0 OD2 A:ASP118 2.8 51.0 1.0 CB A:ASP118 2.8 51.0 1.0 OD2 A:ASP226 2.9 52.0 1.0 CG A:ASP226 2.9 52.0 1.0 CG A:ASP118 3.2 51.0 1.0 C5' A:GTP401 4.2 50.7 1.0 NH2 A:ARG21 4.2 34.4 1.0 CA A:ASP118 4.3 51.0 1.0 CB A:ASP226 4.4 52.0 1.0 OD1 A:ASP118 4.5 51.0 1.0 NZ A:LYS31 4.5 39.5 1.0 O A:ASP118 4.6 51.0 1.0 CA A:GLY228 4.7 40.3 1.0 C A:ASP118 4.7 51.0 1.0 N A:GLY228 4.9 40.3 1.0

Magnesium binding site 2 out of 6 in the Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:48.9 occ:1.00 OD1 B:ASP226 2.2 50.0 1.0 OD2 B:ASP226 2.6 50.0 1.0 OD2 B:ASP118 2.6 50.2 1.0 CB B:ASP118 2.7 50.2 1.0 CG B:ASP226 2.7 50.0 1.0 CG B:ASP118 3.0 50.2 1.0 CA B:ASP118 4.1 50.2 1.0 C5' B:GTP401 4.2 50.3 1.0 CB B:ASP226 4.2 50.0 1.0 NH2 B:ARG21 4.2 32.8 1.0 OD1 B:ASP118 4.3 50.2 1.0 O B:ASP118 4.4 50.2 1.0 N B:GLY228 4.5 38.7 1.0 CA B:GLY228 4.5 38.7 1.0 C B:ASP118 4.5 50.2 1.0 NZ B:LYS31 4.7 38.5 1.0 CA B:ASP226 5.0 50.0 1.0 N B:ASP118 5.0 50.2 1.0

Magnesium binding site 3 out of 6 in the Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:46.7 occ:1.00 CB C:ASP118 3.2 49.8 1.0 OD2 C:ASP118 3.3 49.8 1.0 CG C:ASP118 3.7 49.8 1.0 CB C:ASP226 3.9 53.0 1.0 NH2 C:ARG21 4.1 32.0 1.0 OD2 C:ASP226 4.2 53.0 1.0 C5' C:GTP401 4.3 51.4 1.0 CG C:ASP226 4.5 53.0 1.0 CA C:GLY228 4.6 37.3 1.0 NZ C:LYS31 4.6 38.9 1.0 CA C:ASP118 4.6 49.8 1.0 N C:GLY228 4.6 37.3 1.0 O C:ASP118 4.8 49.8 1.0 OD1 C:ASP118 4.9 49.8 1.0 C C:ASP118 4.9 49.8 1.0 CA C:ASP226 5.0 53.0 1.0

Magnesium binding site 4 out of 6 in the Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:49.0 occ:1.00 OD1 D:ASP226 2.3 51.6 1.0 OD2 D:ASP226 2.6 51.6 1.0 OD2 D:ASP118 2.7 50.6 1.0 CB D:ASP118 2.8 50.6 1.0 CG D:ASP226 2.8 51.6 1.0 CG D:ASP118 3.2 50.6 1.0 C5' D:GTP401 4.2 50.3 1.0 NH2 D:ARG21 4.2 34.6 1.0 CA D:ASP118 4.2 50.6 1.0 CB D:ASP226 4.3 51.6 1.0 OD1 D:ASP118 4.4 50.6 1.0 O D:ASP118 4.5 50.6 1.0 CA D:GLY228 4.5 39.8 1.0 N D:GLY228 4.5 39.8 1.0 NZ D:LYS31 4.6 39.1 1.0 C D:ASP118 4.6 50.6 1.0 CA D:ASP226 5.0 51.6 1.0

Magnesium binding site 5 out of 6 in the Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:49.6 occ:1.00 OD2 E:ASP118 2.3 50.9 1.0 CB E:ASP118 2.6 50.9 1.0 CG E:ASP118 2.9 50.9 1.0 CB E:ASP226 4.0 53.2 1.0 OD1 E:ASP118 4.1 50.9 1.0 CA E:ASP118 4.1 50.9 1.0 OD2 E:ASP226 4.2 53.2 1.0 C5' E:GTP401 4.2 50.3 1.0 NH2 E:ARG21 4.3 33.1 1.0 CG E:ASP226 4.5 53.2 1.0 CA E:GLY228 4.5 38.5 1.0 NZ E:LYS31 4.5 38.4 1.0 N E:GLY228 4.5 38.5 1.0 C E:ASP118 4.6 50.9 1.0 O E:ASP118 4.6 50.9 1.0 N E:ASP118 4.9 50.9 1.0

Magnesium binding site 6 out of 6 in the Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:50.0 occ:1.00 OD2 F:ASP226 2.3 50.8 1.0 OD1 F:ASP226 2.4 50.8 1.0 CG F:ASP226 2.6 50.8 1.0 CB F:ASP118 3.2 49.4 1.0 OD2 F:ASP118 3.3 49.4 1.0 CG F:ASP118 3.7 49.4 1.0 NH2 F:ARG21 4.1 32.3 1.0 CB F:ASP226 4.2 50.8 1.0 C5' F:GTP401 4.3 51.4 1.0 NZ F:LYS31 4.5 39.0 1.0 CA F:ASP118 4.6 49.4 1.0 CA F:GLY228 4.7 38.1 1.0 O F:ASP118 4.8 49.4 1.0 OD1 F:ASP118 4.9 49.4 1.0 C F:ASP118 4.9 49.4 1.0 N F:GLY228 4.9 38.1 1.0 CA F:ASP226 4.9 50.8 1.0

H.Li, T.Ji, Q.Sun, Y.Chen, W.Xu, C.Huang. Structural Insights Into Selective Inhibition of Leishmanial Gdp-Mannose Pyrophosphorylase. Cell Discov V. 8 83 2022.
ISSN: ESSN 2056-5968
PubMed: 36038534
DOI: 10.1038/S41421-022-00424-Z