Sodium in PDB 7scm: Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2

The structure of Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2, PDB code: 7scm was solved by C.R.Nisler, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.93 / 2.27
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.109, 73.109, 381.934, 90, 90, 120
R / Rfree (%)	19 / 23.8

The structure of Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2 also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Calcium	(Ca)	6 atoms

The binding sites of Sodium atom in the Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2 (pdb code 7scm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2, PDB code: 7scm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2


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 Ancestral Amniote Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:28.9 occ:1.00 OD1 A:ASP69 2.3 32.7 1.0 OD2 A:ASP102 2.3 27.7 1.0 OE1 A:GLU71 2.3 24.3 1.0 OE1 A:GLU19 2.4 22.1 1.0 O A:HOH500 2.6 27.6 1.0 CG A:ASP102 3.0 26.2 1.0 OD1 A:ASP102 3.1 22.8 1.0 CD A:GLU19 3.2 22.8 1.0 CG A:ASP69 3.4 32.9 1.0 O A:HOH506 3.4 42.4 1.0 OE2 A:GLU19 3.5 20.6 1.0 CD A:GLU71 3.6 27.0 1.0 CA A:CA301 3.8 19.5 1.0 OD2 A:ASP69 4.1 37.5 1.0 N A:ARG70 4.1 25.3 1.0 CA A:ASP69 4.2 27.8 1.0 ND2 A:ASN103 4.2 23.0 1.0 CB A:ASP69 4.2 29.4 1.0 O A:HOH443 4.3 32.4 1.0 O A:HOH414 4.4 27.7 1.0 OE2 A:GLU71 4.4 25.2 1.0 CG A:GLU19 4.4 23.9 1.0 CB A:GLU71 4.4 29.3 1.0 N A:GLU71 4.4 29.6 1.0 CG A:GLU71 4.5 27.4 1.0 C A:ASP69 4.5 24.4 1.0 CB A:ASP102 4.5 24.0 1.0 O A:HOH428 4.5 34.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2


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 Ancestral Amniote Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:37.1 occ:1.00 OD2 B:ASP102 2.1 33.1 1.0 OD1 B:ASP69 2.4 43.7 1.0 OE1 B:GLU71 2.4 30.9 1.0 OE1 B:GLU19 2.5 27.7 1.0 O B:HOH463 2.5 31.4 1.0 CG B:ASP102 3.0 31.3 1.0 OD1 B:ASP102 3.2 30.7 1.0 CD B:GLU19 3.2 28.6 1.0 CG B:ASP69 3.3 42.1 1.0 CD B:GLU71 3.5 31.8 1.0 OE2 B:GLU19 3.6 27.3 1.0 CA B:CA302 3.9 24.9 1.0 OD2 B:ASP69 4.0 49.4 1.0 CA B:ASP69 4.1 35.2 1.0 CB B:ASP69 4.1 35.9 1.0 ND2 B:ASN103 4.2 30.2 1.0 N B:ARG70 4.2 32.7 1.0 CB B:GLU71 4.2 34.9 1.0 CG B:GLU71 4.3 34.2 1.0 CB B:ASP102 4.3 27.6 1.0 OE2 B:GLU71 4.4 31.5 1.0 N B:GLU71 4.4 35.9 1.0 CG B:GLU19 4.4 28.6 1.0 C B:ASP69 4.5 33.2 1.0 O B:HOH462 4.7 37.1 1.0 CA B:GLU71 5.0 37.3 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:31.4 occ:1.00 O B:SER26 2.3 23.1 1.0 O A:ILE7 2.4 27.7 1.0 OG B:SER26 2.4 26.9 1.0 O B:HOH453 2.4 32.3 1.0 O A:HOH427 2.6 29.4 1.0 O A:HOH416 2.6 29.8 1.0 C B:SER26 3.3 25.6 1.0 C A:ILE7 3.4 24.5 1.0 CB B:SER26 3.5 26.0 1.0 N B:SER26 3.7 25.4 1.0 CA B:SER26 3.7 25.9 1.0 CA A:ILE7 3.9 24.6 1.0 O A:ASN8 4.1 23.8 1.0 C A:ASN8 4.3 22.8 1.0 O B:HOH430 4.4 30.1 1.0 N B:VAL27 4.5 24.9 1.0 N A:ASN8 4.5 25.0 1.0 OD2 A:ASP12 4.5 48.3 1.0 CG2 A:ILE7 4.6 27.4 1.0 N A:TYR9 4.6 21.8 1.0 O A:PHE6 4.7 24.3 1.0 C B:SER25 4.7 25.5 1.0 CB B:SER25 4.8 30.1 1.0 CA A:TYR9 4.8 21.5 1.0 CB A:ILE7 4.9 26.2 1.0 CA B:VAL27 5.0 28.0 1.0 CA A:ASN8 5.0 23.8 1.0

C.R.Nisler, M.Sotomayor. Crystal Structure of Ancestral Amniote Cadherin-23 EC1-2 To Be Published.