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

Enzymatic activity of 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;

Magnesium Binding Sites:

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 7d72

Go back to Magnesium Binding Sites List in 7d72
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 7d72

Go back to Magnesium Binding Sites List in 7d72
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 7d72

Go back to Magnesium Binding Sites List in 7d72
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

Reference:

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.
Page generated: Sun Jul 11 16:29:58 2021

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