Manganese in PDB 8e60: X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Occluded, Manganese-Bound State

The structure of X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Occluded, Manganese-Bound State, PDB code: 8e60 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)	41.28 / 2.38
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.076, 71.101, 98.747, 90, 90, 90
R / Rfree (%)	20.8 / 25.9

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

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Occluded, Manganese-Bound State (pdb code 8e60). 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 Wt in An Occluded, Manganese-Bound State, PDB code: 8e60:
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 Wt in An Occluded, 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 Wt in An Occluded, Manganese-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:63.7 occ:0.60 O A:ALA53 2.2 66.9 1.0 O A:HOH605 2.3 52.2 1.0 OD1 A:ASN59 2.3 70.0 1.0 O A:ALA227 2.5 46.2 1.0 OD1 A:ASP56 2.7 64.9 1.0 SD A:MET230 2.8 78.8 1.0 C A:ALA53 3.4 79.1 1.0 CG A:ASN59 3.5 54.3 1.0 O A:HOH639 3.5 57.8 1.0 CG A:ASP56 3.5 56.5 1.0 C A:ALA227 3.6 49.8 1.0 CA A:TYR54 3.6 106.0 1.0 CE A:MET230 3.7 58.7 1.0 N A:TYR54 3.9 103.8 1.0 CG A:MET230 3.9 56.8 1.0 C A:TYR54 4.0 102.6 1.0 ND2 A:ASN59 4.1 54.1 1.0 CA A:ALA227 4.1 43.7 1.0 OD2 A:ASP56 4.2 56.4 1.0 CB A:ASP56 4.4 52.5 1.0 N A:ASP56 4.4 58.0 1.0 N A:MET55 4.4 80.6 1.0 CB A:ALA227 4.4 39.2 1.0 O A:TYR54 4.5 102.0 1.0 CA A:ALA53 4.6 74.8 1.0 CB A:ASN59 4.7 56.5 1.0 N A:THR228 4.7 41.5 1.0 OE1 A:GLN378 4.8 40.5 1.0 N A:ASN59 4.8 44.7 1.0 CB A:TYR54 4.8 111.2 1.0 CA A:ASP56 5.0 48.3 1.0 CB A:ALA53 5.0 71.0 1.0

Manganese binding site 2 out of 2 in the X-Ray Structure of the Deinococcus Radiodurans Nramp/Mnth Divalent Transition Metal Transporter Wt in An Occluded, 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 Wt in An Occluded, Manganese-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:75.4 occ:1.00 OD2 A:ASP296 2.1 69.0 1.0 O A:HOH619 2.3 64.4 1.0 OD2 A:ASP369 2.3 67.7 1.0 O A:HOH642 2.7 85.5 1.0 CG A:ASP296 2.8 63.8 1.0 OD1 A:ASP296 2.9 65.5 1.0 CG A:ASP369 2.9 56.3 1.0 OD1 A:ASP369 2.9 58.6 1.0 OG A:SER371 3.7 55.8 1.0 CD A:PRO370 3.9 60.4 1.0 CG2 A:THR298 4.0 72.0 1.0 CB A:SER371 4.2 49.9 1.0 CB A:ASP369 4.3 55.6 1.0 N A:SER371 4.3 40.1 1.0 CB A:ASP296 4.3 52.4 1.0 N A:PRO370 4.5 55.2 1.0 O A:HOH628 4.5 67.8 1.0 C3 A:PEG528 4.6 82.6 1.0 OG1 A:THR298 4.6 68.1 1.0 CA A:ASP369 4.7 60.9 1.0 C A:ASP369 4.9 50.3 1.0 CG A:PRO370 4.9 51.1 1.0 CA A:SER371 4.9 50.8 1.0 CB A:THR298 5.0 66.0 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