Sodium in PDB 8e5v: X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wtsoak in An Occluded State

The structure of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wtsoak in An Occluded State, PDB code: 8e5v 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)	41.23 / 2.36
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.954, 71.037, 98.773, 90, 90, 90
R / Rfree (%)	21.7 / 24.6

The structure of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wtsoak in An Occluded State also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wtsoak in An Occluded State (pdb code 8e5v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wtsoak in An Occluded State, PDB code: 8e5v:

Sodium binding site 1 out of 1 in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wtsoak in An Occluded State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wtsoak in An Occluded State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:51.3 occ:1.00 O A:HOH647 2.3 60.8 1.0 OD2 A:ASP296 2.3 75.8 1.0 O A:HOH635 2.4 81.1 1.0 OD2 A:ASP369 2.4 74.7 1.0 CG A:ASP369 2.9 65.1 1.0 OD1 A:ASP296 3.0 83.2 1.0 O A:HOH631 3.0 72.2 1.0 OD1 A:ASP369 3.0 60.8 1.0 CG A:ASP296 3.0 76.2 1.0 CD A:PRO370 3.6 62.9 1.0 OG A:SER371 3.8 57.8 1.0 O2 A:PEG531 3.9 98.4 1.0 N A:SER371 4.0 52.9 1.0 N A:PRO370 4.1 57.0 1.0 O A:HOH641 4.1 65.3 1.0 CG2 A:THR298 4.1 79.6 1.0 CB A:SER371 4.2 62.2 1.0 CB A:ASP369 4.2 64.4 1.0 C3 A:PEG531 4.4 87.6 1.0 CG A:PRO370 4.5 60.4 1.0 CB A:ASP296 4.5 69.4 1.0 CA A:ASP369 4.5 63.9 1.0 C A:ASP369 4.6 57.7 1.0 CB A:PRO370 4.7 56.3 1.0 CA A:SER371 4.7 53.3 1.0 CA A:PRO370 4.8 56.8 1.0 O A:HOH609 4.9 92.2 1.0 OG1 A:THR298 4.9 80.4 1.0 C A:PRO370 4.9 53.2 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