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

The binding sites of Magnesium atom in the Cryo-Em Structure of Leishmanial Gdp-Mannose Pyrophosphorylase in Complex with Gdp-Mannose (pdb code 7wht). 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 Gdp-Mannose, PDB code: 7wht:
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 Gdp-Mannose


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 Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:99.5 occ:1.00 O2A A:GDD601 2.0 104.1 1.0 OD2 A:ASP118 2.0 90.2 1.0 O3A A:GDD601 2.4 104.1 1.0 PA A:GDD601 2.5 104.1 1.0 OD1 A:ASP226 2.5 93.8 1.0 CG A:ASP118 2.9 90.2 1.0 O1A A:GDD601 3.1 104.1 1.0 OD1 A:ASP118 3.2 90.2 1.0 CG A:ASP226 3.3 93.8 1.0 O3B A:GDD601 3.3 104.1 1.0 OD2 A:ASP226 3.3 93.8 1.0 PB A:GDD601 3.5 104.1 1.0 O51 A:GDD601 3.7 104.1 1.0 O5' A:GDD601 3.9 104.1 1.0 O1B A:GDD601 4.1 104.1 1.0 C11 A:GDD601 4.3 104.1 1.0 CB A:ASP118 4.3 90.2 1.0 NZ A:LYS31 4.4 86.4 1.0 C61 A:GDD601 4.5 104.1 1.0 O6A A:GDD601 4.5 104.1 1.0 C5' A:GDD601 4.5 104.1 1.0 C3' A:GDD601 4.5 104.1 1.0 C51 A:GDD601 4.5 104.1 1.0 O2B A:GDD601 4.7 104.1 1.0 CB A:ASP226 4.8 93.8 1.0 C2' A:GDD601 4.8 104.1 1.0

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


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 Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:98.0 occ:1.00 OD2 B:ASP118 2.0 91.3 1.0 O2A B:GDD601 2.1 104.0 1.0 OD1 B:ASP226 2.5 95.2 1.0 CG B:ASP118 2.7 91.3 1.0 OD1 B:ASP118 2.7 91.3 1.0 OD2 B:ASP226 2.8 95.2 1.0 PA B:GDD601 3.0 104.0 1.0 CG B:ASP226 3.0 95.2 1.0 O3A B:GDD601 3.0 104.0 1.0 O1A B:GDD601 3.7 104.0 1.0 O51 B:GDD601 3.9 104.0 1.0 O3B B:GDD601 4.1 104.0 1.0 CB B:ASP118 4.1 91.3 1.0 PB B:GDD601 4.2 104.0 1.0 O5' B:GDD601 4.3 104.0 1.0 NZ B:LYS31 4.3 86.5 1.0 O6A B:GDD601 4.3 104.0 1.0 C61 B:GDD601 4.4 104.0 1.0 C3' B:GDD601 4.4 104.0 1.0 CB B:ASP226 4.5 95.2 1.0 O B:ASP118 4.6 91.3 1.0 C2' B:GDD601 4.6 104.0 1.0 ND2 B:ASN116 4.6 95.3 1.0 C51 B:GDD601 4.6 104.0 1.0 C11 B:GDD601 4.7 104.0 1.0 O1B B:GDD601 4.7 104.0 1.0 C5' B:GDD601 4.8 104.0 1.0 C B:ASP118 5.0 91.3 1.0

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


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 Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:98.3 occ:1.00 OD2 C:ASP118 2.0 89.5 1.0 O2A C:GDD601 2.1 102.8 1.0 O3A C:GDD601 2.4 102.8 1.0 PA C:GDD601 2.4 102.8 1.0 OD1 C:ASP226 2.6 93.3 1.0 CG C:ASP118 3.0 89.5 1.0 O1A C:GDD601 3.1 102.8 1.0 OD1 C:ASP118 3.3 89.5 1.0 O3B C:GDD601 3.3 102.8 1.0 PB C:GDD601 3.4 102.8 1.0 CG C:ASP226 3.4 93.3 1.0 OD2 C:ASP226 3.5 93.3 1.0 O51 C:GDD601 3.6 102.8 1.0 O5' C:GDD601 3.9 102.8 1.0 O1B C:GDD601 4.0 102.8 1.0 C11 C:GDD601 4.1 102.8 1.0 NZ C:LYS31 4.2 83.8 1.0 CB C:ASP118 4.4 89.5 1.0 C5' C:GDD601 4.4 102.8 1.0 C3' C:GDD601 4.5 102.8 1.0 O6A C:GDD601 4.5 102.8 1.0 O2B C:GDD601 4.6 102.8 1.0 C51 C:GDD601 4.6 102.8 1.0 C61 C:GDD601 4.7 102.8 1.0 C2' C:GDD601 4.8 102.8 1.0 CB C:ASP226 4.8 93.3 1.0 C4' C:GDD601 5.0 102.8 1.0 ND2 C:ASN116 5.0 94.2 1.0

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


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 Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:100.1 occ:1.00 OD2 D:ASP118 2.0 90.7 1.0 O2A D:GDD601 2.0 103.6 1.0 O3A D:GDD601 2.5 103.6 1.0 PA D:GDD601 2.5 103.6 1.0 OD1 D:ASP226 2.5 94.0 1.0 CG D:ASP118 3.0 90.7 1.0 O1A D:GDD601 3.0 103.6 1.0 OD1 D:ASP118 3.2 90.7 1.0 CG D:ASP226 3.3 94.0 1.0 OD2 D:ASP226 3.3 94.0 1.0 O3B D:GDD601 3.3 103.6 1.0 PB D:GDD601 3.5 103.6 1.0 O51 D:GDD601 3.8 103.6 1.0 O5' D:GDD601 3.9 103.6 1.0 O1B D:GDD601 4.2 103.6 1.0 C11 D:GDD601 4.3 103.6 1.0 CB D:ASP118 4.3 90.7 1.0 NZ D:LYS31 4.4 86.1 1.0 O6A D:GDD601 4.5 103.6 1.0 C5' D:GDD601 4.5 103.6 1.0 C3' D:GDD601 4.6 103.6 1.0 C61 D:GDD601 4.6 103.6 1.0 C51 D:GDD601 4.6 103.6 1.0 O2B D:GDD601 4.7 103.6 1.0 CB D:ASP226 4.7 94.0 1.0 C2' D:GDD601 4.9 103.6 1.0

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


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 Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:99.4 occ:1.00 OD2 E:ASP118 2.0 91.6 1.0 O2A E:GDD601 2.1 104.8 1.0 OD1 E:ASP226 2.7 95.4 1.0 PA E:GDD601 2.7 104.8 1.0 O3A E:GDD601 2.8 104.8 1.0 OD2 E:ASP226 2.8 95.4 1.0 CG E:ASP118 2.9 91.6 1.0 OD1 E:ASP118 3.0 91.6 1.0 CG E:ASP226 3.1 95.4 1.0 O1A E:GDD601 3.4 104.8 1.0 O3B E:GDD601 3.7 104.8 1.0 PB E:GDD601 3.8 104.8 1.0 O51 E:GDD601 3.9 104.8 1.0 O5' E:GDD601 4.1 104.8 1.0 NZ E:LYS31 4.2 86.3 1.0 CB E:ASP118 4.3 91.6 1.0 O1B E:GDD601 4.5 104.8 1.0 O6A E:GDD601 4.5 104.8 1.0 C3' E:GDD601 4.5 104.8 1.0 C61 E:GDD601 4.5 104.8 1.0 C11 E:GDD601 4.5 104.8 1.0 CB E:ASP226 4.6 95.4 1.0 C51 E:GDD601 4.7 104.8 1.0 C5' E:GDD601 4.7 104.8 1.0 C2' E:GDD601 4.7 104.8 1.0 ND2 E:ASN116 4.8 95.6 1.0 O E:ASP118 4.9 91.6 1.0

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


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 Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg602 b:96.5 occ:1.00 O2A F:GDD601 2.1 102.1 1.0 OD2 F:ASP118 2.1 88.6 1.0 O3A F:GDD601 2.4 102.1 1.0 PA F:GDD601 2.4 102.1 1.0 OD1 F:ASP226 2.5 91.4 1.0 CG F:ASP118 2.9 88.6 1.0 O1A F:GDD601 3.1 102.1 1.0 OD1 F:ASP118 3.2 88.6 1.0 O3B F:GDD601 3.3 102.1 1.0 CG F:ASP226 3.3 91.4 1.0 PB F:GDD601 3.4 102.1 1.0 OD2 F:ASP226 3.4 91.4 1.0 O51 F:GDD601 3.7 102.1 1.0 O5' F:GDD601 3.9 102.1 1.0 O1B F:GDD601 4.1 102.1 1.0 NZ F:LYS31 4.1 83.9 1.0 C11 F:GDD601 4.2 102.1 1.0 CB F:ASP118 4.4 88.6 1.0 C3' F:GDD601 4.4 102.1 1.0 C5' F:GDD601 4.4 102.1 1.0 O6A F:GDD601 4.5 102.1 1.0 C51 F:GDD601 4.6 102.1 1.0 O2B F:GDD601 4.6 102.1 1.0 C61 F:GDD601 4.7 102.1 1.0 C2' F:GDD601 4.7 102.1 1.0 CB F:ASP226 4.8 91.4 1.0 C4' F:GDD601 5.0 102.1 1.0 ND2 F:ASN116 5.0 93.2 1.0 O F:ASP118 5.0 88.6 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