Sodium in PDB 6nd8: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium, PDB code: 6nd8 was solved by J.Stetefeld, M.D.Mcdougall, P.C.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 2.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	131.134, 131.134, 251.522, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 30.6

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium also contains other interesting chemical elements:

Barium	(Ba)	6 atoms
Chlorine	(Cl)	9 atoms

The binding sites of Sodium atom in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium (pdb code 6nd8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium, PDB code: 6nd8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:25.0 occ:1.00 O2 B:SO4201 2.1 67.6 1.0 OG C:SER184 3.2 49.9 1.0 S B:SO4201 3.5 95.6 1.0 BA C:BA401 3.5 0.2 1.0 N C:SER184 3.7 48.2 1.0 OG C:SER182 3.9 40.1 1.0 CB C:SER184 3.9 42.5 1.0 O1 B:SO4201 4.0 61.6 1.0 N C:ASN183 4.1 39.0 1.0 O3 B:SO4201 4.3 65.7 1.0 O C:GLY247 4.3 49.4 1.0 O4 B:SO4201 4.3 97.8 1.0 CB C:ASN183 4.3 40.2 1.0 CA C:SER184 4.3 47.8 1.0 CB C:SER182 4.4 37.0 1.0 C C:ASN183 4.5 46.8 1.0 CA C:ASN183 4.6 42.4 1.0 CA C:ASP248 4.7 40.6 1.0 C C:SER182 4.9 38.3 1.0

Sodium binding site 2 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range: probe atom residue distance (Å) B Occ F:Na402 b:26.2 occ:1.00 O1 E:SO4203 2.2 48.0 1.0 OG F:SER184 3.1 44.5 1.0 OG F:SER182 3.4 33.0 1.0 BA F:BA401 3.6 99.2 1.0 N F:SER184 3.6 38.7 1.0 N F:ASN183 3.6 33.9 1.0 S E:SO4203 3.7 81.6 1.0 CB F:SER182 3.7 32.4 1.0 O F:GLY247 3.9 33.5 1.0 CB F:SER184 4.1 33.3 1.0 O4 E:SO4203 4.3 38.1 1.0 CA F:ASN183 4.3 38.0 1.0 CB F:ASN183 4.3 36.9 1.0 O2 E:SO4203 4.3 73.0 1.0 C F:SER182 4.4 29.6 1.0 C F:ASN183 4.4 43.8 1.0 CA F:SER184 4.4 36.8 1.0 O3 E:SO4203 4.5 72.3 1.0 CA F:ASP248 4.5 31.8 1.0 CA F:SER182 4.6 29.3 1.0 C F:GLY247 4.8 29.9 1.0 C F:ASP248 4.9 30.0 1.0

Sodium binding site 3 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range: probe atom residue distance (Å) B Occ I:Na402 b:28.2 occ:1.00 O3 H:SO4202 2.1 54.9 1.0 OG I:SER184 3.1 51.8 1.0 BA I:BA401 3.5 0.6 1.0 S H:SO4202 3.5 91.5 1.0 OG I:SER182 3.6 34.9 1.0 N I:SER184 3.7 41.1 1.0 N I:ASN183 3.8 36.8 1.0 CB I:SER182 4.0 32.9 1.0 O I:GLY247 4.0 37.3 1.0 CB I:SER184 4.0 35.6 1.0 O2 H:SO4202 4.1 43.5 1.0 O1 H:SO4202 4.2 82.4 1.0 O4 H:SO4202 4.4 64.9 1.0 CA I:SER184 4.4 38.4 1.0 CB I:ASN183 4.4 37.3 1.0 CA I:ASN183 4.5 38.9 1.0 C I:ASN183 4.6 45.2 1.0 C I:SER182 4.6 32.2 1.0 CA I:ASP248 4.6 32.6 1.0 CA I:SER182 4.9 30.2 1.0 C I:ASP248 4.9 33.1 1.0 C I:GLY247 5.0 31.5 1.0

Sodium binding site 4 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range: probe atom residue distance (Å) B Occ L:Na402 b:29.2 occ:1.00 O3 K:SO4202 2.2 72.1 1.0 OG L:SER184 3.4 46.1 1.0 BA L:BA401 3.6 0.5 1.0 S K:SO4202 3.6 92.5 1.0 N L:SER184 3.7 47.9 1.0 OG L:SER182 3.8 45.0 1.0 CB L:SER184 3.9 40.8 1.0 O4 K:SO4202 4.0 65.4 1.0 N L:ASN183 4.1 38.8 1.0 O L:GLY247 4.2 46.8 1.0 CB L:SER182 4.3 38.7 1.0 CB L:ASN183 4.3 39.1 1.0 CA L:SER184 4.4 45.2 1.0 O1 K:SO4202 4.4 89.8 1.0 O2 K:SO4202 4.5 60.9 1.0 C L:ASN183 4.5 46.4 1.0 CA L:ASN183 4.6 40.8 1.0 CA L:ASP248 4.6 38.3 1.0 C L:SER182 4.8 35.9 1.0 C L:ASP248 5.0 36.8 1.0

Sodium binding site 5 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range: probe atom residue distance (Å) B Occ O:Na402 b:48.0 occ:1.00 O1 N:SO4201 2.2 0.2 1.0 S N:SO4201 3.6 0.6 1.0 BA O:BA401 3.7 0.1 1.0 N O:SER184 3.7 40.9 1.0 O O:GLY247 3.8 45.3 1.0 OG O:SER182 3.8 56.5 1.0 N O:ASN183 3.9 41.4 1.0 OG O:SER184 4.1 57.5 1.0 O4 N:SO4201 4.1 92.7 1.0 CB O:SER184 4.1 59.3 1.0 O3 N:SO4201 4.1 0.3 1.0 CB O:SER182 4.1 49.6 1.0 CB O:ASN183 4.2 46.0 1.0 CA O:ASN183 4.4 43.4 1.0 CA O:ASP248 4.4 52.5 1.0 CA O:SER184 4.5 47.9 1.0 O2 N:SO4201 4.5 0.8 1.0 C O:ASN183 4.5 43.4 1.0 O O:ASP248 4.6 54.9 1.0 C O:ASP248 4.6 55.0 1.0 CG O:ASN183 4.7 43.9 1.0 C O:SER182 4.8 46.2 1.0 C O:GLY247 4.8 53.9 1.0

Sodium binding site 6 out of 6 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium within 5.0Å range: probe atom residue distance (Å) B Occ R:Na404 b:48.8 occ:1.00 O3 Q:SO4202 2.2 0.6 1.0 N R:SER184 3.5 42.4 1.0 S Q:SO4202 3.6 0.1 1.0 BA R:BA401 3.7 0.3 1.0 OG R:SER184 3.7 52.1 1.0 CB R:SER184 3.9 53.6 1.0 O R:GLY247 3.9 44.5 1.0 N R:ASN183 3.9 38.3 1.0 OG R:SER182 4.0 51.6 1.0 O1 Q:SO4202 4.1 0.9 1.0 CB R:ASN183 4.1 44.4 1.0 CA R:SER184 4.2 46.3 1.0 CB R:SER182 4.2 46.5 1.0 CA R:ASN183 4.3 40.5 1.0 C R:ASN183 4.3 42.0 1.0 O2 Q:SO4202 4.4 0.0 1.0 O4 Q:SO4202 4.4 0.4 1.0 CA R:ASP248 4.6 55.1 1.0 C R:SER182 4.7 43.0 1.0 CG R:ASN183 4.8 42.3 1.0 O R:ASP248 4.8 57.9 1.0 C R:ASP248 4.9 55.1 1.0 C R:GLY247 4.9 54.8 1.0

J.Stetefeld, M.D.Mcdougall, P.C.Loewen. Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Barium To Be Published.