Magnesium in PDB 8j5s: Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- Catalytic Intermediate State

The structure of Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- 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 Pre- Catalytic Intermediate State (pdb code 8j5s). 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 Pre- Catalytic Intermediate State, PDB code: 8j5s:
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 Pre- 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 Pre- Catalytic Intermediate State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:46.5 occ:1.00 OE1 D:GLN445 2.4 47.3 1.0 O2G D:ANP701 2.9 52.0 1.0 N3B D:ANP701 2.9 52.0 1.0 O1G D:ANP701 3.0 52.0 1.0 CB D:SER401 3.0 44.3 1.0 PG D:ANP701 3.0 52.0 1.0 CD D:GLN445 3.4 47.3 1.0 O2A D:ANP701 3.5 52.0 1.0 OG D:SER401 3.6 44.3 1.0 NE2 D:GLN445 3.8 47.3 1.0 O2B D:ANP701 3.9 52.0 1.0 PB D:ANP701 3.9 52.0 1.0 CA D:SER401 4.3 44.3 1.0 OD2 D:ASP524 4.3 45.0 1.0 PA D:ANP701 4.4 52.0 1.0 O3A D:ANP701 4.5 52.0 1.0 N D:SER401 4.5 44.3 1.0 O3G D:ANP701 4.5 52.0 1.0 OD1 D:ASP524 4.5 45.0 1.0 O1A D:ANP701 4.7 52.0 1.0 CG D:GLN445 4.7 47.3 1.0 CG D:ASP524 4.8 45.0 1.0 CB D:GLN445 4.9 47.3 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Mycobacterium Tuberculosis Oppabcd in the Pre- 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 Pre- Catalytic Intermediate State within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg704 b:33.3 occ:1.00 OG D:SER48 2.4 29.3 1.0 OE1 D:GLN96 2.5 35.4 1.0 O2G D:ANP703 2.7 34.3 1.0 CB D:SER48 3.1 29.3 1.0 O2B D:ANP703 3.3 34.3 1.0 CD D:GLN96 3.3 35.4 1.0 N3B D:ANP703 3.4 34.3 1.0 O2A D:ANP703 3.5 34.3 1.0 PG D:ANP703 3.5 34.3 1.0 NE2 D:GLN96 3.6 35.4 1.0 PB D:ANP703 3.9 34.3 1.0 O3G D:ANP703 4.1 34.3 1.0 OD2 D:ASP179 4.2 35.5 1.0 CA D:SER48 4.3 29.3 1.0 PA D:ANP703 4.3 34.3 1.0 N D:SER48 4.4 29.3 1.0 O3A D:ANP703 4.5 34.3 1.0 O1A D:ANP703 4.6 34.3 1.0 CG D:GLN96 4.6 35.4 1.0 CB D:GLN96 4.8 35.4 1.0 OD1 D:ASP179 4.8 35.5 1.0 O1G D:ANP703 4.9 34.3 1.0 CG D:ASP179 5.0 35.5 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