Sodium in PDB 5iu9: Crystal Structure of Zebrafish Protocadherin-19 EC1-4

The structure of Crystal Structure of Zebrafish Protocadherin-19 EC1-4, PDB code: 5iu9 was solved by S.R.Cooper, J.D.Jontes, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.390, 59.776, 165.925, 90.00, 94.39, 90.00
R / Rfree (%)	24.6 / 30.5

The structure of Crystal Structure of Zebrafish Protocadherin-19 EC1-4 also contains other interesting chemical elements:

Calcium

(Ca)

18 atoms

The binding sites of Sodium atom in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4 (pdb code 5iu9). 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 Zebrafish Protocadherin-19 EC1-4, PDB code: 5iu9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1010 b:47.6 occ:1.00 OD1 A:ASN238 2.5 65.1 1.0 O A:THR272 2.7 63.5 1.0 OG1 A:THR272 3.1 68.6 1.0 OD1 A:ASP236 3.3 59.7 1.0 O A:LEU237 3.5 58.6 1.0 OD2 A:ASP236 3.6 62.7 1.0 CG A:ASN238 3.7 64.4 1.0 C A:THR272 3.8 63.8 1.0 CG A:ASP236 3.9 60.5 1.0 CA A:THR272 4.2 66.4 1.0 CB A:THR272 4.3 68.6 1.0 ND2 A:ASN238 4.4 64.9 1.0 C A:LEU237 4.7 57.9 1.0 CB A:ASN238 4.7 62.8 1.0 N A:GLY273 4.9 62.1 1.0 CA A:ASN238 5.0 60.1 1.0 OH A:TYR252 5.0 52.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Zebrafish Protocadherin-19 EC1-4


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 Zebrafish Protocadherin-19 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1010 b:48.9 occ:1.00 O B:THR272 2.5 64.1 1.0 O B:LEU237 2.6 54.5 1.0 OD1 B:ASN238 3.0 59.7 1.0 OD1 B:ASP236 3.2 60.3 1.0 C B:THR272 3.7 64.2 1.0 C B:LEU237 3.8 55.0 1.0 OD2 B:ASP236 3.8 62.6 1.0 CG B:ASP236 3.9 61.0 1.0 CG B:ASN238 4.0 59.5 1.0 CA B:ASN238 4.3 55.4 1.0 CB B:ASN238 4.3 58.3 1.0 N B:ASN238 4.5 55.1 1.0 CA B:THR272 4.5 66.9 1.0 N B:GLY273 4.7 61.9 1.0 N B:LEU237 4.7 56.3 1.0 OH B:TYR252 4.8 59.2 1.0 CA B:GLY273 4.8 60.2 1.0 CA B:LEU237 4.9 55.1 1.0 O B:GLY273 4.9 59.3 1.0 CB B:THR272 4.9 68.8 1.0 C B:GLY273 5.0 60.0 1.0 CE2 B:TYR252 5.0 58.4 1.0

S.R.Cooper, J.D.Jontes, M.Sotomayor. Structural Determinants of Adhesion By Protocadherin-19 and Implications For Its Role in Epilepsy. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27787195
DOI: 10.7554/ELIFE.18529