Calcium 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:

Sodium

(Na)

1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of OBP1 From Varroa Destructor, Form P3<2>21, PDB code: 7nyj:
Jump to Calcium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca203 b:28.5 occ:1.00 OE1 A:GLU117 2.3 44.6 1.0 OE2 A:GLU117 2.5 46.6 1.0 CD A:GLU117 2.7 51.5 1.0 CG A:GLU117 4.2 49.2 1.0 O A:HOH321 4.2 51.6 1.0 CB A:GLU117 4.8 47.1 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of OBP1 From Varroa Destructor, Form P3<2>21 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:17.4 occ:1.00 O A:HOH323 2.2 38.3 1.0 OE2 A:GLU17 2.3 36.0 1.0 OE1 A:GLU17 2.4 34.5 1.0 O A:HOH381 2.6 19.8 1.0 CD A:GLU17 2.7 34.3 1.0 OE2 A:GLU22 4.0 36.4 1.0 O A:HOH314 4.1 31.2 1.0 CG A:GLU17 4.2 33.2 1.0 N A:GLY19 4.3 29.1 1.0 N A:TRP18 4.4 27.7 1.0 CD A:GLU22 4.5 36.8 1.0 O A:GLY19 4.6 27.7 1.0 O A:HOH388 4.7 45.9 1.0 CA A:GLU17 4.7 30.3 1.0 CA A:GLY19 4.8 29.4 1.0 C A:GLU17 4.9 27.8 1.0 CB A:GLU17 5.0 29.5 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