Calcium in PDB 6qm3: Crystal Structure of A Calcium- and Sodium-Bound Mouse Olfactomedin-1 Disulfide-Linked Dimer of the Olfactomedin Domain and Part of Coiled Coil

The structure of Crystal Structure of A Calcium- and Sodium-Bound Mouse Olfactomedin-1 Disulfide-Linked Dimer of the Olfactomedin Domain and Part of Coiled Coil, PDB code: 6qm3 was solved by M.F.Pronker, H.G.Van Den Hoek, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.30 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.705, 46.971, 104.952, 90.00, 117.44, 90.00
R / Rfree (%)	17.9 / 21.6

The structure of Crystal Structure of A Calcium- and Sodium-Bound Mouse Olfactomedin-1 Disulfide-Linked Dimer of the Olfactomedin Domain and Part of Coiled Coil also contains other interesting chemical elements:

Arsenic	(As)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of A Calcium- and Sodium-Bound Mouse Olfactomedin-1 Disulfide-Linked Dimer of the Olfactomedin Domain and Part of Coiled Coil (pdb code 6qm3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Calcium- and Sodium-Bound Mouse Olfactomedin-1 Disulfide-Linked Dimer of the Olfactomedin Domain and Part of Coiled Coil, PDB code: 6qm3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Calcium- and Sodium-Bound Mouse Olfactomedin-1 Disulfide-Linked Dimer of the Olfactomedin Domain and Part of Coiled Coil


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Calcium- and Sodium-Bound Mouse Olfactomedin-1 Disulfide-Linked Dimer of the Olfactomedin Domain and Part of Coiled Coil within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:16.2 occ:1.00 OD1 A:ASP453 2.3 40.9 1.0 O A:LEU452 2.4 19.7 1.0 OE1 A:GLU404 2.4 37.7 1.0 O A:ALA405 2.4 16.3 1.0 OD2 A:ASP356 2.5 26.5 1.0 O A:HOH616 2.7 39.3 1.0 CG A:ASP356 3.3 33.2 1.0 CD A:GLU404 3.4 32.5 1.0 CG A:ASP453 3.4 49.9 1.0 OD1 A:ASP356 3.5 34.9 1.0 C A:LEU452 3.5 20.3 1.0 C A:ALA405 3.6 24.1 1.0 OE2 A:GLU404 3.7 44.6 1.0 CE A:MET358 4.1 43.8 1.0 N A:ALA405 4.2 16.6 1.0 CA A:ASP453 4.2 26.6 1.0 OD2 A:ASP453 4.3 56.7 1.0 N A:LEU452 4.3 21.6 1.0 N A:ASP453 4.3 25.3 1.0 NA A:NA507 4.3 42.6 1.0 CB A:ASP453 4.3 34.0 1.0 OH A:TYR347 4.4 26.6 1.0 CA A:LEU452 4.5 17.8 1.0 CA A:ALA405 4.5 15.9 1.0 N A:PHE406 4.5 22.9 1.0 CA A:PHE406 4.6 19.2 1.0 CG A:GLU404 4.7 25.2 1.0 CB A:PHE406 4.7 22.1 1.0 CB A:ASP356 4.8 38.5 1.0 O A:HOH619 4.8 44.2 1.0 O A:HOH610 4.9 35.0 1.0 CE2 A:TYR347 4.9 20.4 1.0 SD A:MET358 4.9 43.5 1.0 CB A:GLU404 4.9 16.4 1.0 CB A:LEU452 4.9 23.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Calcium- and Sodium-Bound Mouse Olfactomedin-1 Disulfide-Linked Dimer of the Olfactomedin Domain and Part of Coiled Coil


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Calcium- and Sodium-Bound Mouse Olfactomedin-1 Disulfide-Linked Dimer of the Olfactomedin Domain and Part of Coiled Coil within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:57.2 occ:1.00 O B:HOH645 2.3 62.4 1.0 OD2 B:ASP356 2.6 66.0 1.0 O B:ALA405 2.6 31.7 1.0 O B:LEU452 2.6 35.8 1.0 OE1 B:GLU404 2.9 60.3 1.0 OD1 B:ASP453 3.4 74.3 1.0 CG B:ASP356 3.5 59.4 1.0 C B:LEU452 3.6 31.9 1.0 OD1 B:ASP356 3.7 67.6 1.0 C B:ALA405 3.9 30.3 1.0 CE B:MET358 3.9 42.5 1.0 CD B:GLU404 4.1 58.2 1.0 CG B:ASP453 4.2 70.9 1.0 NA B:NA506 4.2 58.7 1.0 N B:LEU452 4.3 27.2 1.0 O B:HOH618 4.3 50.6 1.0 CA B:ASP453 4.4 38.5 1.0 N B:ASP453 4.5 36.0 1.0 N B:ALA405 4.5 33.8 1.0 CA B:LEU452 4.5 29.8 1.0 CA B:PHE406 4.7 22.8 1.0 OE2 B:GLU404 4.7 58.1 1.0 OH B:TYR347 4.7 63.0 1.0 CB B:PHE406 4.7 26.9 1.0 N B:PHE406 4.7 24.5 1.0 SD B:MET358 4.8 40.5 1.0 CA B:ALA405 4.8 22.5 1.0 CB B:LEU452 4.8 32.1 1.0 OD2 B:ASP453 4.8 74.7 1.0 CE2 B:TYR347 4.9 65.5 1.0 CB B:ASP356 4.9 41.0 1.0 CB B:ASP453 4.9 55.6 1.0

M.F.Pronker, H.Van Den Hoek, B.J.C.Janssen. Design and Structural Characterisation of Olfactomedin-1 Variants As Tools For Functional Studies. Bmc Mol Cell Biol V. 20 50 2019.
ISSN: ISSN 2661-8850
PubMed: 31726976
DOI: 10.1186/S12860-019-0232-1