Magnesium in PDB 7d72: Cryo-Em Structures of Human Gmppa/Gmppb Complex Bound to Gdp-Mannose

All present enzymatic activity of Cryo-Em Structures of Human Gmppa/Gmppb Complex Bound to Gdp-Mannose:
2.7.7.13;

The binding sites of Magnesium atom in the Cryo-Em Structures of Human Gmppa/Gmppb Complex Bound to Gdp-Mannose (pdb code 7d72). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structures of Human Gmppa/Gmppb Complex Bound to Gdp-Mannose, PDB code: 7d72:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structures of Human Gmppa/Gmppb Complex Bound to 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 Structures of Human Gmppa/Gmppb Complex Bound to Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:88.0 occ:1.00 OD1 E:ASP110 2.1 114.6 1.0 O3B E:GDD401 2.1 122.9 1.0 O E:HOH502 2.1 76.1 1.0 O2A E:GDD401 2.5 122.9 1.0 O E:HOH501 2.6 99.8 1.0 OD1 E:ASP218 2.8 111.9 1.0 CG E:ASP110 3.3 114.6 1.0 PB E:GDD401 3.3 122.9 1.0 O3A E:GDD401 3.5 122.9 1.0 PA E:GDD401 3.6 122.9 1.0 CG E:ASP218 3.9 111.9 1.0 NZ E:LYS23 3.9 92.8 1.0 O6A E:GDD401 4.0 122.9 1.0 OD2 E:ASP110 4.1 114.6 1.0 O2B E:GDD401 4.2 122.9 1.0 CB E:ASP110 4.3 114.6 1.0 OD2 E:ASP218 4.3 111.9 1.0 O51 E:GDD401 4.5 122.9 1.0 O1B E:GDD401 4.5 122.9 1.0 O5' E:GDD401 4.6 122.9 1.0 O1A E:GDD401 4.6 122.9 1.0 CA E:GLY220 4.7 90.7 1.0 C5' E:GDD401 4.7 122.9 1.0 C11 E:GDD401 5.0 122.9 1.0 C51 E:GDD401 5.0 122.9 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structures of Human Gmppa/Gmppb Complex Bound to 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 Structures of Human Gmppa/Gmppb Complex Bound to Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:86.9 occ:1.00 O3B F:GDD401 2.0 118.9 1.0 OD1 F:ASP110 2.3 101.6 1.0 O F:HOH501 2.3 100.7 1.0 O2A F:GDD401 2.3 118.9 1.0 O F:HOH502 2.7 102.8 1.0 PB F:GDD401 3.2 118.9 1.0 OD1 F:ASP218 3.3 86.9 1.0 OD2 F:ASP218 3.3 86.9 1.0 CG F:ASP110 3.5 101.6 1.0 PA F:GDD401 3.6 118.9 1.0 O3A F:GDD401 3.6 118.9 1.0 CG F:ASP218 3.7 86.9 1.0 NZ F:LYS23 3.7 82.6 1.0 O2B F:GDD401 3.9 118.9 1.0 O6A F:GDD401 4.1 118.9 1.0 OD2 F:ASP110 4.2 101.6 1.0 C5' F:GDD401 4.5 118.9 1.0 CB F:ASP110 4.5 101.6 1.0 O5' F:GDD401 4.5 118.9 1.0 O1B F:GDD401 4.5 118.9 1.0 O51 F:GDD401 4.5 118.9 1.0 CA F:GLY220 4.6 70.5 1.0 O1A F:GDD401 4.7 118.9 1.0 CE F:LYS23 4.9 82.6 1.0 N F:GLY220 5.0 70.5 1.0 C51 F:GDD401 5.0 118.9 1.0 C11 F:GDD401 5.0 118.9 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structures of Human Gmppa/Gmppb Complex Bound to 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 Structures of Human Gmppa/Gmppb Complex Bound to Gdp-Mannose within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:107.0 occ:1.00 O G:HOH502 2.3 90.7 1.0 O G:HOH501 2.3 102.5 1.0 OD1 G:ASP218 2.4 91.9 1.0 CG G:ASP218 3.2 91.9 1.0 OD2 G:ASP218 3.3 91.9 1.0 OD1 G:ASP110 3.5 100.5 1.0 CA G:GLY220 3.5 85.8 1.0 O3B G:GDD401 3.9 105.2 1.0 N G:GLY220 4.0 85.8 1.0 C G:GLY220 4.1 85.8 1.0 N G:GLN221 4.2 82.2 1.0 O2A G:GDD401 4.3 105.2 1.0 CG G:ASP110 4.5 100.5 1.0 CB G:ASP218 4.6 91.9 1.0 CG G:GLN221 4.8 82.2 1.0 CB G:ASP110 4.9 100.5 1.0 NH1 G:ARG13 5.0 91.9 1.0

L.Zheng, Z.Liu, Y.Wang, F.Yang, J.Wang, J.Qing, X.Cai, X.Mo, N.Gao, D.Jia. Cryo-Em Structures of Human Gmppa/Gmppb Complex Reveal How Cells Maintain Gdp-Mannose Homeostasis To Be Published.