Magnesium in PDB 9g2k: Cryo-Em Structure of Irtab in Outward-Occluded State in Nanodisc in Complex with Adp-Vanadate

The structure of Cryo-Em Structure of Irtab in Outward-Occluded State in Nanodisc in Complex with Adp-Vanadate also contains other interesting chemical elements:

Vanadium	(V)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Magnesium atom in the Cryo-Em Structure of Irtab in Outward-Occluded State in Nanodisc in Complex with Adp-Vanadate (pdb code 9g2k). 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 Nanodisc in Complex with Adp-Vanadate, PDB code: 9g2k:
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 Nanodisc in Complex with Adp-Vanadate


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 Nanodisc in Complex with Adp-Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:26.1 occ:1.00 OG A:SER694 1.9 31.1 1.0 O1B A:AOV1001 2.0 36.4 1.0 O1G A:AOV1001 2.0 37.3 1.0 OE1 A:GLN735 2.1 45.6 1.0 HG A:SER694 2.5 34.8 1.0 HE22 A:GLN735 2.7 44.3 1.0 HB2 A:SER694 2.7 34.4 1.0 CB A:SER694 2.8 31.0 1.0 CD A:GLN735 2.8 45.6 1.0 NE2 A:GLN735 3.0 48.9 1.0 VG A:AOV1001 3.2 59.6 1.0 HB3 A:SER694 3.2 33.9 1.0 PB A:AOV1001 3.3 46.7 1.0 H B:GLY470 3.5 62.4 1.0 O3G A:AOV1001 3.6 31.7 1.0 O3B A:AOV1001 3.8 34.9 1.0 H A:SER694 3.8 35.1 1.0 O1A A:AOV1001 3.8 21.3 1.0 HE21 A:GLN735 3.8 43.6 1.0 HB2 A:GLN735 3.9 42.0 1.0 HB2 B:SER469 3.9 61.3 1.0 CA A:SER694 4.1 27.3 1.0 O3A A:AOV1001 4.1 41.2 1.0 CG A:GLN735 4.1 40.7 1.0 N A:SER694 4.3 31.2 1.0 N B:GLY470 4.3 58.3 1.0 HA B:SER469 4.4 60.9 1.0 CB A:GLN735 4.4 42.1 1.0 O2B A:AOV1001 4.4 32.1 1.0 HA A:SER694 4.4 33.0 1.0 OD1 A:ASP814 4.4 42.0 1.0 PA A:AOV1001 4.5 19.7 1.0 HB3 A:GLN735 4.5 42.9 1.0 HG2 A:GLN735 4.7 43.1 1.0 HG3 A:GLN735 4.7 42.1 1.0 OD2 A:ASP814 4.7 53.0 1.0 O2A A:AOV1001 4.7 35.8 1.0 HA3 B:GLY470 4.8 62.9 1.0 CB B:SER469 4.8 61.9 1.0 OE1 A:GLU815 4.8 43.6 1.0 HG3 A:GLU815 4.8 40.3 1.0 O4G A:AOV1001 4.9 37.6 1.0 HB2 A:LYS693 4.9 36.0 1.0 O2G A:AOV1001 4.9 40.6 1.0 CA B:SER469 4.9 54.9 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Irtab in Outward-Occluded State in Nanodisc in Complex with Adp-Vanadate


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 Nanodisc in Complex with Adp-Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:57.1 occ:1.00 HG1 B:THR371 1.7 60.7 1.0 O2B B:AOV601 1.9 50.4 1.0 OE1 B:GLN412 1.9 69.3 1.0 OG1 B:THR371 2.0 63.6 1.0 CD B:GLN412 2.6 66.4 1.0 HE22 B:GLN412 2.6 65.8 1.0 PB B:AOV601 2.7 51.0 1.0 NE2 B:GLN412 2.9 71.2 1.0 O3B B:AOV601 2.9 54.5 1.0 O1B B:AOV601 3.0 50.4 1.0 CB B:THR371 3.3 58.0 1.0 HB B:THR371 3.5 59.0 1.0 OD1 B:ASP492 3.6 71.5 1.0 HE21 B:GLN412 3.6 65.4 1.0 H B:THR371 3.7 60.0 1.0 HB2 B:GLN412 3.7 65.1 1.0 OE1 B:GLU493 3.7 80.9 1.0 CG B:GLN412 3.8 58.0 1.0 HG21 B:THR371 4.0 58.6 1.0 O3G B:AOV601 4.0 42.1 1.0 HG3 B:GLN412 4.0 64.2 1.0 OD2 B:ASP492 4.1 79.1 1.0 HG3 B:LYS370 4.2 61.2 1.0 N B:THR371 4.2 44.6 1.0 CB B:GLN412 4.2 62.9 1.0 O3A B:AOV601 4.2 37.8 1.0 CG2 B:THR371 4.2 56.9 1.0 CG B:ASP492 4.3 75.0 1.0 CA B:THR371 4.3 52.3 1.0 H A:GLY792 4.4 37.6 1.0 HA B:THR371 4.5 58.0 1.0 HB3 B:GLN412 4.5 64.7 1.0 HG11 B:VAL522 4.5 64.0 1.0 HG2 B:GLN412 4.6 63.6 1.0 VG B:AOV601 4.6 63.2 1.0 O2A B:AOV601 4.7 59.4 1.0 HG3 B:GLU493 4.8 70.2 1.0 O1A B:AOV601 4.8 49.6 1.0 CD B:GLU493 4.8 77.8 1.0 HG23 B:THR371 4.8 58.9 1.0 HG13 B:VAL522 4.8 63.6 1.0 HE1 B:HIS524 4.8 70.7 1.0 PA B:AOV601 4.9 51.2 1.0 HE2 B:LYS370 4.9 61.4 1.0 HB2 A:SER791 4.9 42.4 1.0 HG22 B:THR371 4.9 60.0 1.0 O2G B:AOV601 5.0 57.1 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