Magnesium in PDB 9iqg: Cryo-Em Structure of MSRV1273C/72C From Mycobacterium Smegmatis in the Atp|Adp+VI-Bound Occ (VI) State

The structure of Cryo-Em Structure of MSRV1273C/72C From Mycobacterium Smegmatis in the Atp|Adp+VI-Bound Occ (VI) State also contains other interesting chemical elements:

Vanadium

(V)

1 atom

The binding sites of Magnesium atom in the Cryo-Em Structure of MSRV1273C/72C From Mycobacterium Smegmatis in the Atp|Adp+VI-Bound Occ (VI) State (pdb code 9iqg). 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 MSRV1273C/72C From Mycobacterium Smegmatis in the Atp|Adp+VI-Bound Occ (VI) State, PDB code: 9iqg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of MSRV1273C/72C From Mycobacterium Smegmatis in the Atp|Adp+VI-Bound Occ (VI) 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 MSRV1273C/72C From Mycobacterium Smegmatis in the Atp|Adp+VI-Bound Occ (VI) State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:40.6 occ:1.00 OE1 A:GLN416 1.9 53.7 1.0 OG A:SER375 1.9 51.5 1.0 O3B A:ATP601 2.6 56.0 1.0 O3G A:ATP601 2.8 54.6 1.0 O2B A:ATP601 3.0 53.9 1.0 CB A:SER375 3.0 46.2 1.0 CD A:GLN416 3.1 47.5 1.0 PG A:ATP601 3.4 51.5 1.0 PB A:ATP601 3.4 49.6 1.0 NE2 A:GLN416 3.8 49.9 1.0 O1A A:ATP601 3.9 53.1 1.0 N A:SER375 4.0 47.6 1.0 CA A:SER375 4.0 44.9 1.0 O3A A:ATP601 4.2 48.3 1.0 O2G A:ATP601 4.2 52.8 1.0 CG A:GLN416 4.2 40.6 1.0 OD1 A:ASP496 4.4 50.0 1.0 O1G A:ATP601 4.5 57.5 1.0 CB A:GLN416 4.5 42.8 1.0 PA A:ATP601 4.5 51.5 1.0 CB B:ALA530 4.5 44.9 1.0 OD2 A:ASP496 4.6 50.2 1.0 O1B A:ATP601 4.6 56.1 1.0 N B:ALA530 4.7 50.5 1.0 CG A:ASP496 4.9 51.9 1.0 O2A A:ATP601 5.0 58.5 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of MSRV1273C/72C From Mycobacterium Smegmatis in the Atp|Adp+VI-Bound Occ (VI) 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 MSRV1273C/72C From Mycobacterium Smegmatis in the Atp|Adp+VI-Bound Occ (VI) State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:38.5 occ:1.00 OG1 B:THR431 1.9 43.2 1.0 O4 B:VO4702 2.0 51.5 1.0 OE1 B:GLN472 2.0 60.0 1.0 CB B:THR431 3.0 40.3 1.0 CD B:GLN472 3.1 57.6 1.0 CG2 B:THR431 3.6 36.9 1.0 O3B B:ADP701 3.7 44.5 1.0 V B:VO4702 3.8 47.4 1.0 NE2 B:GLN472 3.8 52.2 1.0 O1B B:ADP701 3.8 45.1 1.0 N A:GLY474 4.0 36.0 1.0 CG B:GLN472 4.2 55.2 1.0 CA B:THR431 4.3 39.8 1.0 PB B:ADP701 4.4 42.8 1.0 N B:THR431 4.5 42.1 1.0 CB A:SER473 4.5 32.2 1.0 OD2 B:ASP552 4.5 64.9 1.0 O3 B:VO4702 4.6 40.7 1.0 O2 B:VO4702 4.6 53.9 1.0 CB B:GLN472 4.6 53.6 1.0 O2A B:ADP701 4.6 38.8 1.0 CA A:SER473 4.6 34.2 1.0 OE1 B:GLU553 4.7 63.2 1.0 O1A B:ADP701 4.8 42.0 1.0 CA A:GLY474 4.9 35.4 1.0 C A:SER473 4.9 35.3 1.0 OD1 B:ASP552 4.9 64.8 1.0

J.Yu, Y.Lan, C.Zhu, Z.Chen, J.Pan, Y.Shi, L.Yang, T.Hu, Y.Gao, Y.Zhao, X.Chen, X.Yang, S.Lu, L.W.Guddat, H.Yang, Z.Rao, J.Li. Structure and Mechanism of A Mycobacterial Isoniazid Efflux Pump MSRV1273C/72C with A Degenerate Nucleotide-Binding Site. Nat Commun V. 16 3969 2025.
ISSN: ESSN 2041-1723
PubMed: 40295516
DOI: 10.1038/S41467-025-59300-5