Sodium in PDB 7nyj: Structure of OBP1 From Varroa Destructor, Form P3<2>21

The structure of Structure of OBP1 From Varroa Destructor, Form P3<2>21, PDB code: 7nyj was solved by C.Cambillau, B.Amigues, A.Roussel, P.Leone, A.Gaubert, P.Pelosi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.59 / 1.81
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	53.8, 53.8, 91.67, 90, 90, 120
R / Rfree (%)	18.6 / 22.6

The structure of Structure of OBP1 From Varroa Destructor, Form P3<2>21 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Structure of OBP1 From Varroa Destructor, Form P3<2>21 (pdb code 7nyj). 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 OBP1 From Varroa Destructor, Form P3<2>21, PDB code: 7nyj:

Sodium binding site 1 out of 1 in the Structure of OBP1 From Varroa Destructor, Form P3<2>21


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of OBP1 From Varroa Destructor, Form P3<2>21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:50.0 occ:1.00 OD2 A:ASP121 1.9 69.3 1.0 CG A:ASP121 3.0 60.9 1.0 OD1 A:ASP121 3.5 54.4 1.0 O A:HOH375 4.1 55.2 1.0 CB A:ASP121 4.2 51.9 1.0 CA A:ASP121 5.0 48.6 1.0

B.Amigues, J.Zhu, A.Gaubert, S.Arena, G.Renzone, P.Leone, I.M.Fischer, H.Paulsen, W.Knoll, A.Scaloni, A.Roussel, C.Cambillau, P.Pelosi. A New Non-Classical Fold of Varroa Odorant-Binding Proteins Reveals A Wide Open Internal Cavity. Sci Rep V. 11 13172 2021.
ISSN: ESSN 2045-2322
PubMed: 34162975
DOI: 10.1038/S41598-021-92604-2