Magnesium in PDB 9kwi: Cryo-Em Structure of MSRV1273C/72C(E553Q) Mutant From Mycobacterium Smegmatis in the Atp-Bound Occ State

The binding sites of Magnesium atom in the Cryo-Em Structure of MSRV1273C/72C(E553Q) Mutant From Mycobacterium Smegmatis in the Atp-Bound Occ State (pdb code 9kwi). 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(E553Q) Mutant From Mycobacterium Smegmatis in the Atp-Bound Occ State, PDB code: 9kwi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of MSRV1273C/72C(E553Q) Mutant From Mycobacterium Smegmatis in the Atp-Bound Occ 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(E553Q) Mutant From Mycobacterium Smegmatis in the Atp-Bound Occ State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:37.1 occ:1.00 OG A:SER375 2.0 37.1 1.0 OE1 A:GLN416 2.0 46.7 1.0 O3G A:ATP601 2.1 48.5 1.0 CB A:SER375 3.0 37.6 1.0 PG A:ATP601 3.2 46.5 1.0 O3B A:ATP601 3.2 40.6 1.0 CD A:GLN416 3.2 42.7 1.0 O2B A:ATP601 3.2 44.9 1.0 PB A:ATP601 3.8 47.9 1.0 O1A A:ATP601 3.9 44.2 1.0 O1G A:ATP601 3.9 41.3 1.0 NE2 A:GLN416 4.1 43.9 1.0 CA A:SER375 4.1 34.7 1.0 N A:SER375 4.2 37.1 1.0 CG A:GLN416 4.2 36.6 1.0 O2G A:ATP601 4.3 46.6 1.0 CB B:ALA530 4.4 35.5 1.0 CB A:GLN416 4.4 38.2 1.0 OD1 A:ASP496 4.5 42.8 1.0 O3A A:ATP601 4.5 43.3 1.0 OD2 A:ASP496 4.6 41.3 1.0 N B:ALA530 4.6 37.1 1.0 PA A:ATP601 4.7 40.7 1.0 CG A:ASP496 5.0 41.0 1.0 CB B:SER529 5.0 35.3 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of MSRV1273C/72C(E553Q) Mutant From Mycobacterium Smegmatis in the Atp-Bound Occ 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(E553Q) Mutant From Mycobacterium Smegmatis in the Atp-Bound Occ State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:35.5 occ:1.00 OG1 B:THR431 2.0 33.7 1.0 OE1 B:GLN472 2.0 39.7 1.0 O3G B:ATP702 2.1 45.2 1.0 O2B B:ATP702 2.8 42.7 1.0 CD B:GLN472 2.9 37.6 1.0 CB B:THR431 3.2 31.3 1.0 PG B:ATP702 3.4 41.6 1.0 O3B B:ATP702 3.6 37.8 1.0 NE2 B:GLN472 3.6 37.0 1.0 PB B:ATP702 3.7 42.6 1.0 CG B:GLN472 3.8 39.8 1.0 CG2 B:THR431 3.8 29.8 1.0 O3A B:ATP702 3.9 44.0 1.0 OD1 B:ASP552 4.1 46.3 1.0 O2G B:ATP702 4.3 44.4 1.0 CA B:THR431 4.3 32.2 1.0 OD2 B:ASP552 4.4 47.2 1.0 CB B:GLN472 4.4 39.6 1.0 N B:THR431 4.4 34.0 1.0 N A:GLY474 4.4 30.8 1.0 O1G B:ATP702 4.4 38.6 1.0 CG B:ASP552 4.6 45.1 1.0 OE1 B:GLN553 4.8 30.0 1.0 CB A:SER473 4.8 31.0 1.0 O1A B:ATP702 5.0 39.1 1.0 PA B:ATP702 5.0 39.6 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