Manganese in PDB 8e6i: X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter M230A Mutant in An Inward-Open, Manganese-Bound State

The structure of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter M230A Mutant in An Inward-Open, Manganese-Bound State, PDB code: 8e6i 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)	45.32 / 2.52
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.673, 71.35, 98.593, 90, 90, 90
R / Rfree (%)	22.5 / 26.6

The structure of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter M230A Mutant in An Inward-Open, Manganese-Bound State also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Manganese atom in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter M230A Mutant in An Inward-Open, Manganese-Bound State (pdb code 8e6i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter M230A Mutant in An Inward-Open, Manganese-Bound State, PDB code: 8e6i:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter M230A Mutant in An Inward-Open, Manganese-Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter M230A Mutant in An Inward-Open, Manganese-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:78.8 occ:0.60 O A:HOH639 2.2 108.9 1.0 O A:HOH601 2.3 94.3 1.0 O A:ALA227 2.4 56.7 1.0 O A:HOH643 2.5 80.3 1.0 OD1 A:ASN59 2.6 61.8 1.0 OD1 A:ASP56 2.7 65.1 1.0 O A:TYR54 3.1 111.8 1.0 CG A:ASP56 3.4 58.3 1.0 C A:ALA227 3.5 53.3 1.0 CG A:ASN59 3.7 57.7 1.0 CB A:ASP56 3.9 57.1 1.0 CA A:ALA227 4.1 52.3 1.0 C A:TYR54 4.1 110.9 1.0 ND2 A:ASN59 4.2 58.1 1.0 N A:ASP56 4.2 66.5 1.0 OD2 A:ASP56 4.2 57.0 1.0 CB A:ALA227 4.5 50.4 1.0 N A:THR228 4.6 53.0 1.0 CA A:ASP56 4.7 60.9 1.0 OE1 A:GLN378 4.7 53.2 1.0 CA A:TYR54 4.7 120.6 1.0 O A:HOH604 4.8 94.6 1.0 CB A:ASN59 4.9 56.1 1.0 CA A:THR228 5.0 56.0 1.0 N A:ASN59 5.0 46.0 1.0 CB A:ALA230 5.0 67.9 1.0

Manganese binding site 2 out of 2 in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter M230A Mutant in An Inward-Open, Manganese-Bound State


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter M230A Mutant in An Inward-Open, Manganese-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:71.0 occ:0.80 OD1 A:ASP296 2.6 62.5 1.0 O A:HOH659 2.6 62.5 1.0 OD2 A:ASP369 2.9 68.2 1.0 OD2 A:ASP296 2.9 52.5 1.0 CG A:ASP296 3.1 57.5 1.0 OD1 A:ASP369 3.1 57.0 1.0 CG A:ASP369 3.3 57.8 1.0 CD A:PRO370 3.5 59.4 1.0 OG A:SER371 3.6 49.8 1.0 N A:SER371 3.9 48.1 1.0 N A:PRO370 4.0 53.7 1.0 CG2 A:THR298 4.0 57.3 1.0 CB A:SER371 4.2 49.2 1.0 CG A:PRO370 4.2 51.6 1.0 CB A:PRO370 4.4 52.5 1.0 CB A:ASP369 4.6 54.8 1.0 CB A:ASP296 4.6 58.2 1.0 OG1 A:THR298 4.7 59.3 1.0 CA A:PRO370 4.7 55.6 1.0 CA A:SER371 4.7 49.0 1.0 C A:ASP369 4.7 53.9 1.0 C2 A:PEG528 4.7 69.7 1.0 C A:PRO370 4.8 52.0 1.0 CA A:ASP369 4.8 57.5 1.0 CD1 A:LEU140 4.9 49.1 1.0 N A:LEU297 5.0 49.5 1.0 CB A:THR298 5.0 60.3 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