Sodium in PDB 8umz: Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection

The structure of Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection, PDB code: 8umz was solved by P.De-La-Torre, K.Martinez-Perez, A.Indzhykulian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.20 / 1.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.276, 50.613, 88.263, 90, 94.01, 90
R / Rfree (%)	22.3 / 27.4

The structure of Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Sodium atom in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection (pdb code 8umz). 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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection, PDB code: 8umz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection


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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:15.7 occ:1.00 OE1 A:GLU451 2.3 23.5 1.0 O A:HOH832 2.3 24.4 1.0 OD1 A:ASP449 2.4 27.3 1.0 OD2 A:ASP483 2.5 34.3 1.0 OE1 A:GLU385 2.5 23.7 1.0 O A:HOH821 2.5 24.1 1.0 CG A:ASP483 3.3 28.7 1.0 CD A:GLU385 3.3 22.2 1.0 CG A:ASP449 3.4 25.8 1.0 OD1 A:ASP483 3.4 23.7 1.0 CD A:GLU451 3.5 21.5 1.0 OE2 A:GLU385 3.7 21.0 1.0 OD2 A:ASP449 4.1 29.2 1.0 CA A:CA602 4.1 21.1 1.0 OD1 A:ASN484 4.1 28.9 1.0 N A:ARG450 4.2 22.9 1.0 CB A:ASP449 4.2 24.2 1.0 CA A:ASP449 4.3 24.0 1.0 N A:GLU451 4.3 21.9 1.0 CG A:GLU451 4.4 24.3 1.0 CB A:GLU451 4.4 23.7 1.0 OE2 A:GLU451 4.4 22.4 1.0 CG A:GLU385 4.4 24.1 1.0 O A:HOH761 4.6 32.4 1.0 C A:ASP449 4.6 23.5 1.0 CB A:ASP483 4.8 25.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection


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 Engineered Mouse Protocadherin-15 EC4-EC7 Connection within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:17.3 occ:1.00 OD1 B:ASP449 2.3 28.7 1.0 OE1 B:GLU451 2.3 26.4 1.0 OE1 B:GLU385 2.4 25.0 1.0 O B:HOH775 2.4 30.7 1.0 OD2 B:ASP483 2.5 42.1 1.0 O B:HOH749 2.5 29.4 1.0 CD B:GLU385 3.1 25.5 1.0 CG B:ASP483 3.2 37.0 1.0 CG B:ASP449 3.3 31.2 1.0 OD1 B:ASP483 3.4 32.3 1.0 OE2 B:GLU385 3.4 25.2 1.0 CD B:GLU451 3.5 29.7 1.0 CA B:CA602 3.9 27.6 1.0 OD2 B:ASP449 4.1 40.2 1.0 CA B:ASP449 4.2 31.9 1.0 CB B:ASP449 4.2 31.0 1.0 O B:HOH720 4.3 26.7 1.0 OD1 B:ASN484 4.3 31.7 1.0 CB B:GLU451 4.3 29.0 1.0 CG B:GLU385 4.3 20.3 1.0 N B:GLU451 4.3 30.7 1.0 CG B:GLU451 4.3 27.5 1.0 N B:ARG450 4.3 33.5 1.0 OE2 B:GLU451 4.4 33.0 1.0 C B:ASP449 4.6 32.2 1.0 CB B:ASP483 4.6 36.5 1.0 CA B:GLU451 4.9 31.2 1.0

P.De-La-Torre, K.Martinez-Perez, A.Indzhykulian. Crystal Structure of Engineered Mouse Protocadherin-15 EC4-EC7 Connection To Be Published.