Vanadium in PDB 9g2m: Cryo-Em Structure of Irtab in Outward-Occluded State in Lmng in Complex with Adp-Vanadate

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

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Vanadium atom in the Cryo-Em Structure of Irtab in Outward-Occluded State in Lmng in Complex with Adp-Vanadate (pdb code 9g2m). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Cryo-Em Structure of Irtab in Outward-Occluded State in Lmng in Complex with Adp-Vanadate, PDB code: 9g2m:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in the Cryo-Em Structure of Irtab in Outward-Occluded State in Lmng in Complex with Adp-Vanadate


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Cryo-Em Structure of Irtab in Outward-Occluded State in Lmng in Complex with Adp-Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ A:V1001 b:85.6 occ:1.00 VG A:AOV1001 0.0 85.6 1.0 O4G A:AOV1001 2.1 62.8 1.0 O1G A:AOV1001 2.1 51.3 1.0 O3G A:AOV1001 2.1 59.7 1.0 O2G A:AOV1001 2.1 59.9 1.0 O3B A:AOV1001 2.1 65.3 1.0 HE22 A:GLN735 2.7 60.7 1.0 PB A:AOV1001 3.0 72.3 1.0 MG A:MG1002 3.1 27.2 1.0 O2B A:AOV1001 3.1 65.1 1.0 HE2 A:HIS846 3.2 58.0 1.0 HZ2 A:LYS693 3.2 53.9 1.0 O1B A:AOV1001 3.4 56.2 1.0 NE2 A:GLN735 3.4 62.2 1.0 HZ1 A:LYS693 3.6 52.2 1.0 NZ A:LYS693 3.8 47.8 1.0 NE2 A:HIS846 3.9 54.1 1.0 HE21 A:GLN735 3.9 61.0 1.0 OG A:SER694 4.0 47.1 1.0 H B:GLY471 4.0 54.9 1.0 OE1 A:GLN735 4.1 64.5 1.0 HB2 B:SER469 4.1 55.5 1.0 CD A:GLN735 4.1 66.8 1.0 HG A:SER689 4.2 54.2 1.0 HE2 A:LYS693 4.2 53.2 1.0 H B:GLY470 4.2 57.9 1.0 H A:GLY690 4.4 57.1 1.0 HG A:SER694 4.4 48.1 1.0 HG3 A:GLU815 4.4 58.9 1.0 HA A:SER689 4.4 55.7 1.0 HZ3 A:LYS693 4.5 54.0 1.0 O3A A:AOV1001 4.5 57.9 1.0 HB2 A:LYS693 4.6 53.7 1.0 CE A:LYS693 4.6 50.6 1.0 OE1 A:GLU815 4.6 67.4 1.0 HD2 A:HIS846 4.6 58.6 1.0 HG22 A:ILE844 4.6 51.8 1.0 CD2 A:HIS846 4.6 58.1 1.0 H A:SER694 4.7 48.4 1.0 CE1 A:HIS846 4.8 56.3 1.0 HG21 A:ILE844 4.8 52.5 1.0 N B:GLY471 4.8 53.6 1.0 HE1 A:HIS846 4.9 58.3 1.0 N B:GLY470 4.9 54.5 1.0 HA3 B:GLY470 4.9 57.9 1.0 CD A:GLU815 4.9 63.4 1.0 O B:ALA497 5.0 67.7 1.0 HE3 A:LYS693 5.0 54.1 1.0 HB2 A:SER694 5.0 47.4 1.0 OG A:SER689 5.0 51.6 1.0

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


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Cryo-Em Structure of Irtab in Outward-Occluded State in Lmng in Complex with Adp-Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ B:V601 b:78.4 occ:1.00 VG B:AOV601 0.0 78.4 1.0 O3G B:AOV601 2.1 56.7 1.0 O2G B:AOV601 2.1 66.8 1.0 O1G B:AOV601 2.1 68.5 1.0 O4G B:AOV601 2.1 61.8 1.0 O3B B:AOV601 2.1 60.1 1.0 HE22 B:GLN412 2.5 62.6 1.0 PB B:AOV601 3.0 67.7 1.0 O2B B:AOV601 3.1 70.9 1.0 H A:GLY793 3.2 54.4 1.0 NE2 B:GLN412 3.3 63.3 1.0 O1B B:AOV601 3.3 68.5 1.0 MG B:MG602 3.4 42.0 1.0 HE1 B:HIS524 3.4 83.5 1.0 H B:GLY367 3.5 72.0 1.0 HB2 A:SER791 3.7 55.1 1.0 HE21 B:GLN412 3.8 63.2 1.0 HA B:SER366 3.8 74.5 1.0 HB2 B:SER366 4.0 73.8 1.0 HA3 A:GLY793 4.0 54.5 1.0 N A:GLY793 4.0 52.0 1.0 OE2 B:GLU493 4.1 77.3 1.0 HZ1 B:LYS370 4.2 69.2 1.0 CD B:GLN412 4.2 60.9 1.0 OE1 B:GLN412 4.2 61.0 1.0 CE1 B:HIS524 4.2 81.8 1.0 H A:GLY792 4.3 54.6 1.0 N B:GLY367 4.3 74.5 1.0 OG A:SER791 4.4 48.4 1.0 HZ2 B:LYS370 4.4 69.9 1.0 CB A:SER791 4.5 47.5 1.0 HB3 A:PHE819 4.5 54.4 1.0 HE2 B:LYS370 4.5 69.3 1.0 O3A B:AOV601 4.5 57.9 1.0 CA A:GLY793 4.5 55.4 1.0 CA B:SER366 4.6 74.0 1.0 CB B:SER366 4.6 71.0 1.0 NE2 B:HIS524 4.6 87.3 1.0 NZ B:LYS370 4.7 66.5 1.0 HB3 B:SER366 4.7 74.5 1.0 N A:GLY792 4.7 55.2 1.0 OG1 B:THR371 4.8 71.8 1.0 O A:PHE819 4.9 63.6 1.0 HA3 A:GLY792 4.9 54.0 1.0 HB3 A:SER791 5.0 55.8 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