Magnesium in PDB 8j5t: Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Catalytic Intermediate State

The structure of Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Catalytic Intermediate State also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Catalytic Intermediate State (pdb code 8j5t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Catalytic Intermediate State, PDB code: 8j5t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Catalytic Intermediate State


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 Mycobacterium Tuberculosis Oppabcd in the Catalytic Intermediate State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:47.3 occ:1.00 O3G D:ATP701 2.1 53.3 1.0 OE1 D:GLN445 2.2 48.6 1.0 OG D:SER401 2.2 50.0 1.0 O2B D:ATP701 2.4 53.3 1.0 CB D:SER401 2.7 50.0 1.0 CD D:GLN445 3.1 48.6 1.0 PG D:ATP701 3.3 53.3 1.0 PB D:ATP701 3.4 53.3 1.0 NE2 D:GLN445 3.5 48.6 1.0 O3A D:ATP701 3.6 53.3 1.0 O3B D:ATP701 3.7 53.3 1.0 O2G D:ATP701 3.8 53.3 1.0 CA D:SER401 3.9 50.0 1.0 OD2 D:ASP524 4.0 51.5 1.0 N D:SER401 4.0 50.0 1.0 OD1 D:ASP524 4.1 51.5 1.0 CG D:GLN445 4.4 48.6 1.0 N D:GLY157 4.4 47.1 1.0 CG D:ASP524 4.4 51.5 1.0 O1G D:ATP701 4.6 53.3 1.0 CB D:GLN445 4.6 48.6 1.0 PA D:ATP701 4.7 53.3 1.0 O1B D:ATP701 4.8 53.3 1.0 O1A D:ATP701 4.8 53.3 1.0 CA D:GLY157 4.9 47.1 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Catalytic Intermediate State


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 Mycobacterium Tuberculosis Oppabcd in the Catalytic Intermediate State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:48.4 occ:1.00 OE1 D:GLN96 2.0 52.7 1.0 OG D:SER48 2.1 50.6 1.0 O1G D:ATP703 2.1 53.3 1.0 O2B D:ATP703 2.3 53.3 1.0 CB D:SER48 2.6 50.6 1.0 CD D:GLN96 3.0 52.7 1.0 PG D:ATP703 3.5 53.3 1.0 NE2 D:GLN96 3.5 52.7 1.0 O D:SER501 3.5 48.3 1.0 PB D:ATP703 3.6 53.3 1.0 O2A D:ATP703 3.7 53.3 1.0 O3B D:ATP703 3.8 53.3 1.0 CA D:SER48 4.0 50.6 1.0 O3G D:ATP703 4.1 53.3 1.0 N D:SER48 4.2 50.6 1.0 OD1 D:ASP179 4.2 55.7 1.0 CG D:GLN96 4.3 52.7 1.0 C D:SER501 4.4 48.3 1.0 O3A D:ATP703 4.5 53.3 1.0 PA D:ATP703 4.6 53.3 1.0 O2G D:ATP703 4.6 53.3 1.0 CB D:GLN96 4.7 52.7 1.0 O1B D:ATP703 4.8 53.3 1.0 OD2 D:ASP179 4.8 55.7 1.0 CG D:ASP179 4.9 55.7 1.0 C D:SER48 4.9 50.6 1.0

X.Yang, T.Hu, J.Liang, Z.Xiong, Z.Lin, Y.Zhao, X.Zhou, Y.Gao, S.Sun, X.Yang, L.W.Guddat, H.Yang, Z.Rao, B.Zhang. An Oligopeptide Permease, Oppabcd, Requires An Iron-Sulfur Cluster Domain For Functionality Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01256-Z