Cadmium in PDB 8e6m: X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Inward-Open, Cadmium-Bound State

The structure of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Inward-Open, Cadmium-Bound State, PDB code: 8e6m was solved by S.Ray, R.Gaudet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.54 / 2.48
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.137, 71.369, 99.054, 90, 90, 90
R / Rfree (%)	20.3 / 25

The structure of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Inward-Open, Cadmium-Bound State also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Cadmium atom in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Inward-Open, Cadmium-Bound State (pdb code 8e6m). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Inward-Open, Cadmium-Bound State, PDB code: 8e6m:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Inward-Open, Cadmium-Bound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Inward-Open, Cadmium-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd501 b:83.9 occ:0.60 O A:ALA227 2.8 48.8 1.0 OD1 A:ASN59 2.9 57.0 1.0 O A:TYR54 3.2 104.6 1.0 O A:HOH604 3.2 65.6 1.0 CB A:ASP56 3.2 70.9 1.0 O A:HOH602 3.3 78.3 1.0 SD A:MET230 3.4 90.4 1.0 CG A:MET230 3.5 57.2 1.0 C A:ALA227 3.9 41.9 1.0 CG A:ASN59 3.9 50.5 1.0 N A:ASP56 4.0 73.5 1.0 CG A:ASP56 4.0 80.8 1.0 C A:TYR54 4.2 101.4 1.0 CA A:ASP56 4.3 67.2 1.0 ND2 A:ASN59 4.4 57.0 1.0 CA A:ALA227 4.4 45.4 1.0 OD1 A:ASP56 4.4 89.0 1.0 CA A:TYR54 4.7 104.0 1.0 OD2 A:ASP56 4.8 69.2 1.0 CB A:ALA227 4.8 34.6 1.0 CE A:MET230 4.9 84.0 1.0 CB A:MET230 4.9 67.0 1.0

Cadmium binding site 2 out of 2 in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Inward-Open, Cadmium-Bound State


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Inward-Open, Cadmium-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd502 b:65.0 occ:1.00 OD1 A:ASP296 2.8 67.6 1.0 O A:HOH624 2.8 36.6 1.0 OD2 A:ASP296 2.8 53.8 1.0 OD2 A:ASP369 2.8 72.9 1.0 O A:HOH653 2.9 55.5 1.0 O A:HOH646 2.9 80.1 1.0 OD1 A:ASP369 2.9 53.5 1.0 CG A:ASP296 3.2 63.5 1.0 CG A:ASP369 3.2 59.3 1.0 O A:HOH642 4.0 68.4 1.0 O A:HOH629 4.0 71.3 1.0 OG A:SER371 4.0 50.3 1.0 CG2 A:THR298 4.0 63.7 1.0 CD A:PRO370 4.3 43.7 1.0 OG1 A:THR298 4.3 54.8 1.0 CB A:SER371 4.4 43.8 1.0 CB A:ASP369 4.6 56.0 1.0 N A:SER371 4.6 41.5 1.0 CB A:ASP296 4.6 52.6 1.0 N A:PRO370 4.8 51.7 1.0 CB A:THR298 4.9 55.8 1.0 ND2 A:ASN293 5.0 96.4 1.0 CA A:ASP369 5.0 49.5 1.0

S.Ray, S.P.Berry, E.A.Wilson, C.H.Zhang, M.Shekhar, A.Singharoy, R.Gaudet. High-Resolution Structures with Bound Mn 2+ and Cd 2+ Map the Metal Import Pathway in An Nramp Transporter. Elife V. 12 2023.
ISSN: ESSN 2050-084X
PubMed: 37039477
DOI: 10.7554/ELIFE.84006