Sodium in PDB 8d40: Crystal Structure of Human CELSR1 EC1-4

The structure of Crystal Structure of Human CELSR1 EC1-4, PDB code: 8d40 was solved by E.Tamilselvan, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.24 / 3.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	305.653, 90.356, 94.949, 90, 96.17, 90
R / Rfree (%)	21.6 / 25.2

The structure of Crystal Structure of Human CELSR1 EC1-4 also contains other interesting chemical elements:

Calcium

(Ca)

15 atoms

The binding sites of Sodium atom in the Crystal Structure of Human CELSR1 EC1-4 (pdb code 8d40). 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 Human CELSR1 EC1-4, PDB code: 8d40:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Human CELSR1 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 Human CELSR1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:111.7 occ:1.00 OD2 A:ASP113 1.9 133.5 1.0 OD2 A:ASP77 2.4 125.1 1.0 CG A:ASP113 2.8 136.1 1.0 OD1 A:ASN22 2.9 137.4 1.0 OE1 A:GLU21 2.9 141.5 1.0 CB A:ASP113 3.2 128.8 1.0 CD A:GLU21 3.4 142.6 1.0 CG A:ASP77 3.4 130.1 1.0 OE1 A:GLU79 3.7 124.9 1.0 CG A:GLU21 3.7 131.8 1.0 CG A:ASN22 3.8 145.9 1.0 ND2 A:ASN22 3.9 153.0 1.0 OD1 A:ASP113 4.0 153.1 1.0 CB A:ASP77 4.1 129.8 1.0 OE2 A:GLU21 4.3 166.2 1.0 CA A:CA502 4.4 125.9 1.0 CA A:ASP77 4.4 124.0 1.0 OD1 A:ASP77 4.4 137.9 1.0 CB A:GLU21 4.5 139.8 1.0 CD A:GLU79 4.5 119.3 1.0 OG1 A:THR111 4.6 138.9 1.0 OE2 A:GLU79 4.7 115.0 1.0 CA A:ASP113 4.7 127.2 1.0 NE2 A:HIS114 4.9 128.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Human CELSR1 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 Human CELSR1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:103.7 occ:1.00 OD2 B:ASP113 2.2 149.3 1.0 OE1 B:GLU79 2.5 133.6 1.0 CG B:ASP113 2.6 135.7 1.0 OD1 B:ASP77 2.9 145.3 1.0 OD1 B:ASP113 2.9 135.2 1.0 OE1 B:GLU21 3.0 140.8 1.0 OD2 B:ASP77 3.1 158.3 1.0 CG B:ASP77 3.2 144.1 1.0 CB B:ASP113 3.5 131.7 1.0 CA B:CA501 3.5 108.2 1.0 CD B:GLU21 3.6 139.3 1.0 CD B:GLU79 3.6 132.9 1.0 OE2 B:GLU21 3.7 143.7 1.0 CE1 B:HIS114 3.7 128.1 1.0 ND2 B:ASN22 4.0 143.3 1.0 NE2 B:HIS114 4.0 133.2 1.0 OE2 B:GLU79 4.4 132.6 1.0 ND1 B:HIS114 4.5 123.7 1.0 CG B:GLU79 4.5 135.0 1.0 CB B:ASP77 4.5 136.9 1.0 CB B:GLU79 4.6 132.3 1.0 OD1 B:ASP146 4.7 119.3 1.0 OD1 B:ASN22 4.7 140.9 1.0 CA B:ASP77 4.8 131.5 1.0 CG B:ASN22 4.8 139.8 1.0 CG B:GLU21 4.8 136.2 1.0 N B:ARG78 4.9 119.2 1.0 CD2 B:HIS114 4.9 134.5 1.0 CA B:ASP113 4.9 131.7 1.0 N B:GLU79 5.0 121.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Human CELSR1 EC1-4


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 Human CELSR1 EC1-4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:95.3 occ:1.00 OD1 B:ASP181 2.2 142.4 1.0 OD1 B:ASP219 2.4 138.7 1.0 OD1 B:ASN130 3.0 166.9 1.0 CG B:ASP219 3.1 136.3 1.0 CG B:ASP181 3.2 142.3 1.0 ND2 B:ASN130 3.4 168.3 1.0 OE2 B:GLU129 3.4 139.4 1.0 OE1 B:GLU183 3.6 146.9 1.0 CG B:ASN130 3.6 163.2 1.0 OD2 B:ASP219 3.8 134.4 1.0 CB B:ASP219 3.9 136.6 1.0 OD2 B:ASP181 3.9 136.4 1.0 CB B:ASP181 4.3 142.3 1.0 CD B:GLU183 4.3 149.3 1.0 CD B:GLU129 4.3 154.4 1.0 CA B:ASP181 4.6 138.2 1.0 O B:ASP219 4.6 145.8 1.0 OE2 B:GLU183 4.7 148.1 1.0

E.Tamilselvan, M.Sotomayor. Crystal Structure of Human CELSR1 EC1-4 To Be Published.