Vanadium 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:

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

The binding sites of Vanadium 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 Vanadium atom.
In total 2 binding sites of Vanadium 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 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 Nanodisc 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 Nanodisc in Complex with Adp-Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ A:V1001 b:59.6 occ:1.00 VG A:AOV1001 0.0 59.6 1.0 O2G A:AOV1001 2.1 40.6 1.0 O3G A:AOV1001 2.1 31.7 1.0 O4G A:AOV1001 2.1 37.6 1.0 O3B A:AOV1001 2.1 34.9 1.0 O1G A:AOV1001 2.1 37.3 1.0 HE22 A:GLN735 2.5 44.3 1.0 O1B A:AOV1001 3.0 36.4 1.0 PB A:AOV1001 3.1 46.7 1.0 HE2 A:HIS846 3.2 40.1 1.0 MG A:MG1002 3.2 26.1 1.0 NE2 A:GLN735 3.3 48.9 1.0 H B:GLY471 3.5 59.2 1.0 HZ2 A:LYS693 3.5 37.1 1.0 OE1 A:GLU815 3.7 43.6 1.0 HB2 B:SER469 3.7 61.3 1.0 HE21 A:GLN735 3.8 43.6 1.0 H A:GLY690 3.9 39.7 1.0 O2B A:AOV1001 3.9 32.1 1.0 NE2 A:HIS846 3.9 36.9 1.0 HG A:SER689 3.9 36.7 1.0 H B:GLY470 3.9 62.4 1.0 HE2 A:LYS693 4.0 36.1 1.0 HA A:SER689 4.1 37.0 1.0 HZ1 A:LYS693 4.2 35.5 1.0 NZ A:LYS693 4.2 35.2 1.0 CD A:GLN735 4.2 45.6 1.0 OE1 A:GLN735 4.2 45.6 1.0 CD A:GLU815 4.3 42.1 1.0 N B:GLY471 4.3 57.1 1.0 O3A A:AOV1001 4.4 41.2 1.0 O B:ALA497 4.4 63.3 1.0 N B:GLY470 4.5 58.3 1.0 OG A:SER694 4.5 31.1 1.0 HB3 B:ALA497 4.5 60.8 1.0 CE A:LYS693 4.5 36.7 1.0 HD2 A:HIS846 4.6 40.9 1.0 HA3 B:GLY470 4.6 62.9 1.0 HG3 A:GLU815 4.6 40.3 1.0 HG B:SER469 4.6 61.8 1.0 CD2 A:HIS846 4.6 41.7 1.0 CB B:SER469 4.6 61.9 1.0 HA3 B:GLY471 4.7 59.1 1.0 N A:GLY690 4.7 42.5 1.0 OG A:SER689 4.7 34.1 1.0 HE3 A:LYS693 4.7 36.8 1.0 OE2 A:GLU815 4.8 44.3 1.0 CE1 A:HIS846 4.8 37.4 1.0 OG B:SER469 4.9 65.3 1.0 CA A:SER689 4.9 37.0 1.0 HE1 A:HIS846 4.9 40.2 1.0 HZ3 A:LYS693 4.9 36.2 1.0 HG A:SER694 4.9 34.8 1.0 CA B:GLY470 5.0 64.3 1.0 HB2 A:SER689 5.0 37.1 1.0

Vanadium 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 Vanadium with other atoms in the V 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:V601 b:63.2 occ:1.00 VG B:AOV601 0.0 63.2 1.0 O1G B:AOV601 2.1 62.6 1.0 O4G B:AOV601 2.1 47.9 1.0 O3G B:AOV601 2.1 42.1 1.0 O3B B:AOV601 2.1 54.5 1.0 O2G B:AOV601 2.1 57.1 1.0 H B:GLY367 2.6 71.0 1.0 H A:GLY793 2.8 40.0 1.0 OG B:SER366 3.0 72.0 1.0 HG A:SER791 3.1 43.0 1.0 PB B:AOV601 3.2 51.0 1.0 HA B:SER366 3.2 68.8 1.0 HG B:SER366 3.4 70.3 1.0 O1B B:AOV601 3.4 50.4 1.0 HB2 A:SER791 3.5 42.4 1.0 N B:GLY367 3.5 72.4 1.0 HE22 B:GLN412 3.5 65.8 1.0 HA3 A:GLY793 3.6 39.0 1.0 N A:GLY793 3.7 39.8 1.0 OG A:SER791 3.7 36.0 1.0 CB B:SER366 3.8 63.0 1.0 CA B:SER366 3.8 64.0 1.0 HZ1 B:LYS370 3.9 62.0 1.0 O3A B:AOV601 3.9 37.8 1.0 HB2 B:SER366 4.0 68.9 1.0 HE1 B:HIS524 4.0 70.7 1.0 CB A:SER791 4.1 35.1 1.0 HZ2 B:LYS370 4.1 61.6 1.0 H A:GLY792 4.1 37.6 1.0 CA A:GLY793 4.1 36.7 1.0 C B:SER366 4.2 72.7 1.0 O A:PHE819 4.2 45.2 1.0 HA2 B:GLY367 4.2 71.0 1.0 NE2 B:GLN412 4.4 71.2 1.0 H A:GLU794 4.4 39.7 1.0 O2B B:AOV601 4.4 50.4 1.0 N A:GLY792 4.5 34.2 1.0 NZ B:LYS370 4.5 61.1 1.0 CA B:GLY367 4.5 72.2 1.0 MG B:MG602 4.6 57.1 1.0 CE1 B:HIS524 4.6 71.5 1.0 HE21 B:GLN412 4.7 65.4 1.0 HB3 B:SER366 4.7 69.2 1.0 HB3 A:SER791 4.7 42.8 1.0 HB3 A:PHE819 4.7 36.9 1.0 C A:GLY792 4.8 34.2 1.0 NE2 B:HIS524 4.8 74.5 1.0 HA2 A:GLY793 4.8 39.3 1.0 H B:SER368 4.8 65.1 1.0 HG3 A:GLU794 4.9 41.3 1.0 HA3 A:GLY792 4.9 38.3 1.0 N A:GLU794 5.0 28.4 1.0 C A:SER791 5.0 45.4 1.0 CA A:GLY792 5.0 37.5 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