Magnesium in PDB 9g2x: Cryo-Em Structure of Irtab in Outward-Occluded State in Presence of Mycobactin Under Turnover Conditions in Lmng

The structure of Cryo-Em Structure of Irtab in Outward-Occluded State in Presence of Mycobactin Under Turnover Conditions in Lmng also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Cryo-Em Structure of Irtab in Outward-Occluded State in Presence of Mycobactin Under Turnover Conditions in Lmng (pdb code 9g2x). 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 in Outward-Occluded State in Presence of Mycobactin Under Turnover Conditions in Lmng, PDB code: 9g2x:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Irtab in Outward-Occluded State in Presence of Mycobactin Under Turnover Conditions in Lmng


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 in Outward-Occluded State in Presence of Mycobactin Under Turnover Conditions in Lmng within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:52.3 occ:1.00 H1 A:HOH1102 1.7 42.0 1.0 OE1 A:GLN735 2.0 58.2 1.0 O2G A:ATP1001 2.0 44.7 1.0 O A:HOH1101 2.0 40.6 1.0 O A:HOH1102 2.0 34.8 1.0 H1 A:HOH1101 2.3 45.9 1.0 HE22 A:GLN735 2.3 52.6 1.0 H2 A:HOH1101 2.4 47.0 1.0 HG A:SER694 2.5 41.8 1.0 CD A:GLN735 2.7 55.7 1.0 H2 A:HOH1102 2.7 41.2 1.0 NE2 A:GLN735 2.8 49.8 1.0 O2B A:ATP1001 2.8 53.6 1.0 OG A:SER694 3.0 35.7 1.0 PG A:ATP1001 3.2 47.3 1.0 O3B A:ATP1001 3.4 46.5 1.0 H B:GLY470 3.6 39.8 1.0 HB2 A:SER694 3.6 42.1 1.0 HE21 A:GLN735 3.7 52.6 1.0 PB A:ATP1001 3.7 43.8 1.0 O1G A:ATP1001 3.8 53.2 1.0 HG3 A:GLU815 3.8 55.1 1.0 CB A:SER694 3.9 33.8 1.0 OD1 A:ASP814 3.9 53.4 1.0 HG2 A:GLU815 4.1 55.0 1.0 HB2 B:SER469 4.1 39.0 1.0 CG A:GLN735 4.2 54.5 1.0 HG3 A:LYS693 4.3 47.2 1.0 O3G A:ATP1001 4.4 42.9 1.0 CG A:GLU815 4.4 55.3 1.0 N B:GLY470 4.4 36.5 1.0 OD2 A:ASP814 4.4 56.4 1.0 HG2 A:LYS693 4.5 47.2 1.0 HB3 A:SER694 4.5 41.6 1.0 HA3 B:GLY470 4.5 38.5 1.0 HB2 A:GLN735 4.5 53.1 1.0 O3A A:ATP1001 4.6 37.9 1.0 HB3 A:GLN735 4.6 52.5 1.0 HG2 A:GLN735 4.6 53.5 1.0 CG A:ASP814 4.6 57.3 1.0 HG3 A:GLN735 4.7 53.2 1.0 H A:SER694 4.7 43.9 1.0 HE2 A:HIS846 4.7 52.6 1.0 CB A:GLN735 4.7 53.0 1.0 O1A A:ATP1001 4.8 44.4 1.0 CG A:LYS693 4.8 51.6 1.0 HD2 A:LYS693 4.8 47.1 1.0 H B:GLY471 4.9 43.4 1.0 O1B A:ATP1001 4.9 39.9 1.0 N A:SER694 4.9 45.3 1.0 CA A:SER694 4.9 37.3 1.0 HG21 A:ILE844 5.0 49.9 1.0 CB B:SER469 5.0 37.3 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Irtab in Outward-Occluded State in Presence of Mycobactin Under Turnover Conditions in Lmng


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 in Outward-Occluded State in Presence of Mycobactin Under Turnover Conditions in Lmng within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:50.5 occ:1.00 O B:HOH701 1.9 60.8 1.0 O2B B:ATP601 2.0 60.7 1.0 O B:HOH702 2.0 71.2 1.0 O2G B:ATP601 2.0 67.3 1.0 OE1 B:GLN412 2.2 52.2 1.0 H2 B:HOH701 2.2 60.9 1.0 HG1 B:THR371 2.2 62.0 1.0 H2 B:HOH702 2.4 68.7 1.0 H1 B:HOH702 2.4 68.1 1.0 OG1 B:THR371 2.5 66.0 1.0 H1 B:HOH701 2.7 60.6 1.0 PG B:ATP601 2.9 74.7 1.0 HE22 B:GLN412 2.9 52.8 1.0 CD B:GLN412 3.0 48.1 1.0 PB B:ATP601 3.0 62.5 1.0 O3B B:ATP601 3.1 63.8 1.0 NE2 B:GLN412 3.3 54.0 1.0 HZ2 B:LYS370 3.3 72.3 1.0 O1G B:ATP601 3.3 65.7 1.0 HZ3 B:LYS370 3.4 71.8 1.0 H B:THR371 3.6 63.4 1.0 CB B:THR371 3.7 59.9 1.0 NZ B:LYS370 3.8 74.0 1.0 HB B:THR371 3.8 61.9 1.0 O1B B:ATP601 3.9 65.2 1.0 HB2 B:GLN412 4.0 52.9 1.0 HE21 B:GLN412 4.1 53.3 1.0 OD1 B:ASP492 4.1 63.0 1.0 HB2 B:LYS370 4.1 71.7 1.0 O3A B:ATP601 4.2 59.0 1.0 H A:GLY792 4.2 56.7 1.0 CG B:GLN412 4.2 47.8 1.0 O3G B:ATP601 4.3 60.9 1.0 N B:THR371 4.3 59.0 1.0 HG2 B:GLU493 4.3 67.6 1.0 HZ1 B:LYS370 4.3 71.8 1.0 OD2 B:ASP492 4.3 62.1 1.0 HG3 B:GLU493 4.4 67.7 1.0 HB2 A:SER791 4.5 57.4 1.0 HG21 B:THR371 4.5 60.7 1.0 OE2 B:GLU493 4.5 68.2 1.0 O1A B:ATP601 4.5 55.9 1.0 HG3 B:GLN412 4.6 52.0 1.0 HE2 B:HIS524 4.6 89.2 1.0 CB B:GLN412 4.6 52.0 1.0 CA B:THR371 4.6 57.2 1.0 CG B:ASP492 4.6 64.0 1.0 HE3 B:LYS370 4.7 72.4 1.0 CG2 B:THR371 4.7 52.8 1.0 CG B:GLU493 4.8 72.2 1.0 HG12 B:VAL522 4.8 71.5 1.0 HB3 B:GLN412 4.9 52.9 1.0 CE B:LYS370 4.9 71.5 1.0 HA B:THR371 4.9 61.4 1.0 PA B:ATP601 4.9 58.3 1.0 HG2 B:GLN412 4.9 52.4 1.0 H B:LYS370 5.0 71.8 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