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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

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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

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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

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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

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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

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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

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