Atomistry » Magnesium » PDB 7w8d-7wmb » 7whs
Atomistry »
  Magnesium »
    PDB 7w8d-7wmb »
      7whs »

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

Magnesium Binding Sites:

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 7whs

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

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

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

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

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

Go back to Magnesium Binding Sites List in 7whs
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

Reference:

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
Page generated: Thu Oct 3 11:16:43 2024

Last articles

Cl in 3N06
Cl in 3MZB
Cl in 3MZ9
Cl in 3MZG
Cl in 3MZ0
Cl in 3MZD
Cl in 3MZ1
Cl in 3MYR
Cl in 3MY7
Cl in 3MYX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy