Sodium in PDB 6op6: Structure of Vim-20 in the Reduced State

The structure of Structure of Vim-20 in the Reduced State, PDB code: 6op6 was solved by R.C.Page, B.A.Shurina, J.S.Montgomery, M.G.Orischak, J.C.Nix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.35 / 1.25
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.460, 74.256, 78.693, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.9

The structure of Structure of Vim-20 in the Reduced State also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Sodium atom in the Structure of Vim-20 in the Reduced State (pdb code 6op6). 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 Structure of Vim-20 in the Reduced State, PDB code: 6op6:

Sodium binding site 1 out of 1 in the Structure of Vim-20 in the Reduced State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Vim-20 in the Reduced State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:43.6 occ:1.00 O A:HOH434 2.2 28.7 1.0 O A:HOH461 2.3 36.9 1.0 O A:HOH484 2.5 54.7 1.0 OD1 A:ASP76 3.8 25.4 1.0 OD2 A:ASP76 3.9 27.5 1.0 CG A:ASP76 4.1 22.7 1.0 O A:HOH552 4.2 42.2 1.0 OE1 A:GLU79 4.2 26.6 1.0 OE2 A:GLU79 4.2 38.4 1.0 CD A:GLU79 4.5 33.9 1.0 NH2 A:ARG109 4.5 21.7 1.0 O A:ASP76 4.5 25.0 1.0

Z.Cheng, B.A.Shurina, C.R.Bethel, P.W.Thomas, S.H.Marshall, C.A.Thomas, K.Yang, R.L.Kimble, J.S.Montgomery, M.G.Orischak, C.M.Miller, J.L.Tennenbaum, J.C.Nix, D.L.Tierney, W.Fast, R.A.Bonomo, R.C.Page, M.W.Crowder. A Single Salt Bridge in Vim-20 Increases Protein Stability and Antibiotic Resistance Under Low-Zinc Conditions. Mbio V. 10 2019.
ISSN: ESSN 2150-7511
PubMed: 31744917
DOI: 10.1128/MBIO.02412-19