Magnesium in PDB 9g2p: Cryo-Em Structure of Irtab 2XEQ Mutant in Outward-Occluded State in Nanodisc

The structure of Cryo-Em Structure of Irtab 2XEQ Mutant in Outward-Occluded State in Nanodisc also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Cryo-Em Structure of Irtab 2XEQ Mutant in Outward-Occluded State in Nanodisc (pdb code 9g2p). 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 Irtab 2XEQ Mutant in Outward-Occluded State in Nanodisc, PDB code: 9g2p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Irtab 2XEQ Mutant in Outward-Occluded State in Nanodisc


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 Irtab 2XEQ Mutant in Outward-Occluded State in Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:15.3 occ:1.00 OG A:SER694 2.0 14.8 1.0 OE1 A:GLN735 2.0 23.9 1.0 O3G A:ATP1001 2.3 17.8 1.0 HG A:SER694 2.5 13.7 1.0 O2B A:ATP1001 2.6 17.7 1.0 HB2 A:SER694 2.8 13.8 1.0 CB A:SER694 2.9 13.1 1.0 H B:GLY470 3.1 12.4 1.0 CD A:GLN735 3.1 20.3 1.0 HB3 A:SER694 3.3 12.7 1.0 HB2 B:SER469 3.3 11.7 1.0 O1A A:ATP1001 3.3 13.9 1.0 HE22 A:GLN735 3.4 19.8 1.0 O3B A:ATP1001 3.5 17.2 1.0 PG A:ATP1001 3.5 13.3 1.0 PB A:ATP1001 3.6 11.1 1.0 NE2 A:GLN735 3.7 19.6 1.0 H A:SER694 3.8 15.4 1.0 N B:GLY470 3.9 11.8 1.0 HA B:SER469 4.0 9.7 1.0 HB2 A:GLN735 4.1 20.8 1.0 O3A A:ATP1001 4.1 10.7 1.0 CB B:SER469 4.2 9.7 1.0 CA A:SER694 4.2 10.9 1.0 PA A:ATP1001 4.2 10.2 1.0 N A:SER694 4.4 13.7 1.0 HB3 A:GLN735 4.4 20.9 1.0 O2G A:ATP1001 4.4 23.0 1.0 CG A:GLN735 4.4 21.3 1.0 HB3 B:SER469 4.4 10.5 1.0 HA3 B:GLY470 4.4 11.2 1.0 CA B:SER469 4.5 8.0 1.0 CB A:GLN735 4.5 19.7 1.0 HA A:SER694 4.5 12.3 1.0 HE21 A:GLN735 4.5 19.9 1.0 O1G A:ATP1001 4.6 23.5 1.0 OD1 A:ASP814 4.7 24.3 1.0 OD2 A:ASP814 4.8 24.6 1.0 C B:SER469 4.8 12.5 1.0 CA B:GLY470 4.8 9.3 1.0 O2A A:ATP1001 4.9 19.3 1.0 O1B A:ATP1001 4.9 14.7 1.0 HG2 A:GLN735 4.9 22.7 1.0 H B:GLY471 4.9 11.3 1.0 HG3 A:GLN735 5.0 22.1 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Irtab 2XEQ Mutant in Outward-Occluded State in Nanodisc


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 Irtab 2XEQ Mutant in Outward-Occluded State in Nanodisc within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:10.1 occ:1.00 OG1 B:THR371 1.9 19.4 1.0 OE1 B:GLN412 2.0 29.2 1.0 O1G B:ATP602 2.3 40.1 1.0 O2B B:ATP602 2.4 38.2 1.0 HG1 B:THR371 2.5 17.3 1.0 CD B:GLN412 2.9 18.7 1.0 HB B:THR371 3.0 18.4 1.0 CB B:THR371 3.0 17.5 1.0 HE22 B:GLN412 3.1 24.3 1.0 HG22 B:THR371 3.3 12.7 1.0 NE2 B:GLN412 3.4 23.3 1.0 PG B:ATP602 3.4 35.9 1.0 PB B:ATP602 3.5 17.5 1.0 O3B B:ATP602 3.5 25.4 1.0 H A:GLY792 3.6 21.2 1.0 O1A B:ATP602 3.6 24.9 1.0 CG2 B:THR371 3.7 11.0 1.0 HB2 A:SER791 3.7 18.0 1.0 H B:THR371 4.0 18.2 1.0 HB2 B:GLN412 4.0 19.1 1.0 O3A B:ATP602 4.0 15.7 1.0 HE21 B:GLN493 4.2 33.8 1.0 CA B:THR371 4.2 11.4 1.0 CG B:GLN412 4.2 17.4 1.0 HE21 B:GLN412 4.2 21.1 1.0 PA B:ATP602 4.3 11.9 1.0 OD1 B:ASP492 4.3 30.9 1.0 O3G B:ATP602 4.3 29.4 1.0 OD2 B:ASP492 4.3 16.5 1.0 HG23 B:THR371 4.3 14.5 1.0 HG21 B:THR371 4.3 11.5 1.0 N B:THR371 4.4 13.0 1.0 N A:GLY792 4.4 20.6 1.0 HA A:SER791 4.5 20.9 1.0 CB B:GLN412 4.5 17.5 1.0 HB3 B:GLN412 4.5 18.4 1.0 HA B:THR371 4.5 13.3 1.0 O2G B:ATP602 4.5 25.5 1.0 HE22 B:GLN493 4.6 36.3 1.0 CB A:SER791 4.6 17.5 1.0 HG3 B:GLN412 4.6 17.6 1.0 NE2 B:GLN493 4.6 40.4 1.0 O1B B:ATP602 4.7 32.6 1.0 CG B:ASP492 4.8 26.4 1.0 HB3 A:SER791 4.8 19.1 1.0 O2A B:ATP602 4.9 28.0 1.0 HA3 A:GLY792 4.9 18.8 1.0 HG2 B:GLN412 4.9 19.6 1.0 HG3 B:LYS370 4.9 23.1 1.0 CA A:SER791 5.0 18.6 1.0

I.Gonda, S.Sorrentino, L.Galazzo, N.P.Lichti, F.M.Arnold, A.R.Mehdipour, E.Bordignon, M.A.Seeger. The Mycobacterial Abc Transporter Irtab Employs A Membrane-Facing Crevice For Siderophore-Mediated Iron Uptake Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41467-024-55136-7