Sodium in PDB 7nza: Structure of OBP1 From Varroa Destructor, Form P2<1>

The structure of Structure of OBP1 From Varroa Destructor, Form P2<1>, PDB code: 7nza 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)	38.83 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.604, 112.959, 41.817, 90, 98.95, 90
R / Rfree (%)	17.9 / 20.1

The binding sites of Sodium atom in the Structure of OBP1 From Varroa Destructor, Form P2<1> (pdb code 7nza). 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 P2<1>, PDB code: 7nza:

Sodium binding site 1 out of 1 in the Structure of OBP1 From Varroa Destructor, Form P2<1>


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 P2<1> within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:25.1 occ:1.00 NE A:ARG88 2.7 28.0 1.0 O A:LEU105 2.8 17.7 1.0 OD1 A:ASP109 3.0 18.5 1.0 O A:HOH339 3.1 25.1 1.0 OD2 A:ASP109 3.2 18.8 1.0 CG A:ASP109 3.3 17.1 1.0 CZ A:ARG88 3.5 27.7 1.0 NH2 A:ARG88 3.5 29.6 1.0 CD A:ARG88 3.6 24.6 1.0 C A:LEU105 3.6 16.3 1.0 CB A:LEU105 3.8 17.5 1.0 CD2 A:HIS108 3.8 16.1 1.0 CA A:LEU105 3.9 16.6 1.0 CG A:ARG88 4.1 21.7 1.0 CD2 A:LEU105 4.2 21.4 1.0 CB A:HIS108 4.3 14.8 1.0 CG A:HIS108 4.4 15.5 1.0 CG A:LEU105 4.5 19.5 1.0 N A:ASP109 4.5 14.6 1.0 CB A:ASP109 4.6 16.1 1.0 N A:LEU106 4.6 15.9 1.0 NH1 A:ARG88 4.8 29.3 1.0 NE2 A:HIS108 4.9 15.8 1.0 O A:HOH381 4.9 20.9 1.0 CD1 A:LEU105 5.0 20.9 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