Sodium 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
Calcium	(Ca)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na507 b:42.6 occ:1.00 O A:LEU357 2.3 40.0 1.0 O A:HOH619 2.3 44.2 1.0 OD2 A:ASP453 2.3 56.7 1.0 OD1 A:ASP356 2.5 34.9 1.0 O A:GLY302 3.1 41.6 1.0 CG A:ASP453 3.1 49.9 1.0 OD1 A:ASP453 3.3 40.9 1.0 O A:GLN303 3.3 43.0 1.0 C A:LEU357 3.4 34.6 1.0 C A:GLY302 3.4 34.7 1.0 CG A:ASP356 3.7 33.2 1.0 CA A:GLY302 3.7 22.8 1.0 O A:HOH618 3.8 36.0 1.0 N A:LEU357 3.8 36.6 1.0 O A:HOH616 3.9 39.3 1.0 C A:GLN303 4.1 30.9 1.0 N A:GLN303 4.2 28.3 1.0 CA A:LEU357 4.2 30.0 1.0 CB A:MET358 4.3 34.0 1.0 OD2 A:ASP356 4.3 26.5 1.0 CA A:CA506 4.3 16.2 1.0 N A:MET358 4.3 34.3 1.0 CA A:MET358 4.4 34.8 1.0 C A:ASP356 4.4 34.0 1.0 CB A:ASP453 4.4 34.0 1.0 CE A:MET358 4.5 43.8 1.0 O A:THR301 4.5 29.4 1.0 CA A:ASP356 4.7 30.2 1.0 CA A:GLN303 4.7 29.7 1.0 CB A:ASP356 4.8 38.5 1.0 CB A:VAL304 4.8 31.7 1.0 N A:VAL304 4.9 29.4 1.0 N A:GLY302 5.0 22.4 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na506 b:58.7 occ:1.00 O B:LEU357 2.3 37.7 1.0 OD2 B:ASP453 2.6 74.7 1.0 O B:HOH621 2.7 41.4 1.0 OD1 B:ASP356 2.7 67.6 1.0 OD1 B:ASP453 3.1 74.3 1.0 CG B:ASP453 3.2 70.9 1.0 C B:LEU357 3.4 31.1 1.0 O B:GLN303 3.4 31.7 1.0 O B:HOH645 3.5 62.4 1.0 O B:GLY302 3.8 38.5 1.0 CG B:ASP356 3.8 59.4 1.0 C B:GLY302 3.9 32.7 1.0 CA B:GLY302 4.0 25.1 1.0 N B:LEU357 4.1 34.9 1.0 CA B:MET358 4.1 32.8 1.0 N B:MET358 4.2 29.5 1.0 CA B:CA505 4.2 57.2 1.0 CB B:MET358 4.2 30.4 1.0 C B:GLN303 4.3 26.4 1.0 OD2 B:ASP356 4.3 66.0 1.0 CA B:LEU357 4.3 28.3 1.0 N B:GLN303 4.5 31.8 1.0 CB B:ASP453 4.7 55.6 1.0 CB B:VAL304 4.7 33.0 1.0 C B:ASP356 4.7 32.6 1.0 CE B:MET358 4.7 42.5 1.0 O B:HOH606 4.9 41.0 1.0 O B:THR301 4.9 31.2 1.0 CA B:GLN303 5.0 25.8 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