Sodium in PDB 7n86: Crystal Structure of Human Protocadherin-24 EC1-2 Form II

The structure of Crystal Structure of Human Protocadherin-24 EC1-2 Form II, PDB code: 7n86 was solved by D.Modak, M.E.Gray, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.15 / 3.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.899, 86.641, 104.892, 90, 103.46, 90
R / Rfree (%)	21.4 / 29

The structure of Crystal Structure of Human Protocadherin-24 EC1-2 Form II also contains other interesting chemical elements:

Calcium	(Ca)	14 atoms
Chlorine	(Cl)	6 atoms
Iodine	(I)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II (pdb code 7n86). 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 Human Protocadherin-24 EC1-2 Form II, PDB code: 7n86:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


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 Human Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:20.0 occ:1.00 OD1 A:ASP66 2.2 49.6 1.0 OE1 A:GLU68 2.2 30.8 1.0 OE2 A:GLU17 2.3 36.1 1.0 OD2 A:ASP99 2.3 41.4 1.0 OD1 A:ASP99 2.6 38.8 1.0 CG A:ASP99 2.7 35.0 1.0 CG A:ASP66 2.9 44.1 1.0 CD A:GLU17 3.1 29.3 1.0 OD2 A:ASP66 3.1 38.5 1.0 OE1 A:GLU17 3.3 30.1 1.0 CD A:GLU68 3.4 35.1 1.0 ND2 A:ASN100 3.5 34.7 1.0 CA A:CA303 3.6 33.7 1.0 OE2 A:GLU68 3.8 33.3 1.0 CB A:ASP66 4.0 45.2 1.0 N A:TYR67 4.0 38.4 1.0 CA A:ASP66 4.1 42.3 1.0 CB A:ASP99 4.1 31.5 1.0 CG A:GLU17 4.4 29.0 1.0 CG A:ASN100 4.5 30.6 1.0 C A:ASP66 4.5 38.3 1.0 CG A:GLU68 4.6 39.5 1.0 N A:GLU68 4.6 39.2 1.0 CB A:GLU68 4.8 41.3 1.0 OD1 A:ASN100 4.9 42.0 1.0 OD1 A:ASP96 4.9 54.3 1.0 CB A:GLU17 5.0 29.4 1.0 CA A:TYR67 5.0 38.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


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 Human Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:37.2 occ:1.00 OD2 B:ASP99 2.0 41.5 1.0 OD1 B:ASP66 2.7 70.2 1.0 OD2 B:ASP66 2.7 51.6 1.0 CG B:ASP66 2.7 50.7 1.0 CG B:ASP99 2.9 35.2 1.0 OE2 B:GLU17 2.9 31.0 1.0 OE1 B:GLU68 3.1 32.3 1.0 OD1 B:ASP99 3.5 38.0 1.0 CD B:GLU17 3.7 34.5 1.0 CB B:ASP66 3.7 36.8 1.0 CB B:ASP99 3.8 32.0 1.0 CA B:ASP66 4.0 33.2 1.0 OE1 B:GLU17 4.3 38.5 1.0 CD B:GLU68 4.3 40.2 1.0 O B:LEU65 4.5 39.8 1.0 ND2 B:ASN100 4.5 34.5 1.0 CG B:GLU17 4.6 33.8 1.0 CA B:CA302 4.6 27.6 1.0 N B:TYR67 4.8 32.5 1.0 OE2 B:GLU68 4.8 45.7 1.0 C B:ASP66 4.9 35.0 1.0

M.E.Gray, Z.R.Johnson, D.Modak, T.J.Tyska, M.Sotomayor. Species-Dependent Heterophilic and Homophilic Cadherin Interactions in Intestinal Intermicrovillar Links To Be Published.