Sodium in PDB 6nd9: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium, PDB code: 6nd9 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)	48.06 / 2.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	131.044, 131.044, 251.245, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 27.2

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

Chlorine	(Cl)	3 atoms
Calcium	(Ca)	6 atoms

The binding sites of Sodium atom in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium (pdb code 6nd9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium, PDB code: 6nd9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium


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 with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:28.6 occ:1.00 O3 C:SO4402 1.8 60.5 1.0 OG C:SER184 2.8 30.4 1.0 S C:SO4402 3.3 91.6 1.0 N C:SER184 3.3 44.0 1.0 CA C:CA401 3.4 45.9 1.0 CB C:SER184 3.6 30.0 1.0 OG C:SER182 3.6 31.7 1.0 O4 C:SO4402 3.9 0.1 1.0 O1 C:SO4402 3.9 52.6 1.0 CA C:SER184 3.9 37.5 1.0 N C:ASN183 3.9 39.9 1.0 CB C:SER182 4.0 35.1 1.0 O2 C:SO4402 4.1 47.1 1.0 O C:GLY247 4.1 40.6 1.0 C C:ASN183 4.3 39.3 1.0 CB C:ASN183 4.4 40.8 1.0 CA C:ASN183 4.4 40.3 1.0 C C:SER182 4.6 36.3 1.0 CA C:ASP248 4.8 42.2 1.0 CA C:SER182 4.9 32.5 1.0

Sodium binding site 2 out of 5 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium


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 with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ F:Na402 b:21.2 occ:1.00 O3 E:SO4203 2.0 65.6 1.0 OG F:SER184 2.8 30.4 1.0 CA F:CA401 3.3 33.4 1.0 S E:SO4203 3.3 91.0 1.0 OG F:SER182 3.3 25.7 1.0 O4 E:SO4203 3.4 96.5 1.0 N F:SER184 3.5 38.1 1.0 CB F:SER182 3.6 30.5 1.0 CB F:SER184 3.7 27.8 1.0 N F:ASN183 3.8 30.7 1.0 O F:GLY247 3.9 31.9 1.0 O2 E:SO4203 4.1 46.2 1.0 CA F:SER184 4.1 28.9 1.0 O1 E:SO4203 4.2 51.1 1.0 C F:ASN183 4.4 37.7 1.0 C F:SER182 4.4 28.1 1.0 CA F:ASN183 4.4 33.4 1.0 CB F:ASN183 4.5 34.7 1.0 CA F:SER182 4.6 27.9 1.0 CA F:ASP248 4.7 28.7 1.0 C F:GLY247 5.0 27.9 1.0 C F:ASP248 5.0 30.1 1.0

Sodium binding site 3 out of 5 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium


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 with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ I:Na402 b:26.9 occ:1.00 O3 H:SO4202 1.9 68.0 1.0 OG I:SER184 2.8 36.8 1.0 S H:SO4202 3.2 94.9 1.0 CA I:CA401 3.2 34.3 1.0 OG I:SER182 3.3 27.0 1.0 O4 H:SO4202 3.4 83.7 1.0 N I:SER184 3.5 39.1 1.0 CB I:SER182 3.7 29.5 1.0 CB I:SER184 3.7 30.3 1.0 O2 H:SO4202 3.9 47.1 1.0 N I:ASN183 3.9 30.0 1.0 O I:GLY247 4.0 36.6 1.0 CA I:SER184 4.2 30.2 1.0 O1 H:SO4202 4.3 51.6 1.0 C I:ASN183 4.5 39.8 1.0 C I:SER182 4.5 26.2 1.0 CA I:ASN183 4.5 33.1 1.0 CB I:ASN183 4.5 31.7 1.0 CA I:ASP248 4.7 28.2 1.0 CA I:SER182 4.7 26.0 1.0 C I:ASP248 5.0 30.9 1.0

Sodium binding site 4 out of 5 in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium


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 with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ L:Na403 b:26.7 occ:1.00 O3 L:SO4402 1.8 59.0 1.0 OG L:SER184 2.7 33.0 1.0 S L:SO4402 3.2 92.5 1.0 CA L:CA401 3.3 43.7 1.0 N L:SER184 3.4 44.2 1.0 OG L:SER182 3.5 34.4 1.0 CB L:SER184 3.5 30.7 1.0 O1 L:SO4402 3.8 60.9 1.0 CB L:SER182 3.9 35.4 1.0 CA L:SER184 4.0 36.6 1.0 O4 L:SO4402 4.0 86.1 1.0 N L:ASN183 4.0 38.1 1.0 O2 L:SO4402 4.1 50.1 1.0 O L:GLY247 4.2 36.7 1.0 C L:ASN183 4.4 38.4 1.0 CB L:ASN183 4.5 39.5 1.0 CA L:ASN183 4.5 38.0 1.0 C L:SER182 4.6 35.6 1.0 CA L:SER182 4.9 32.7 1.0 CA L:ASP248 4.9 39.5 1.0

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


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 with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ O:Na402 b:26.6 occ:1.00 O4 N:SO4201 2.2 72.6 1.0 OG O:SER184 2.9 40.7 1.0 S N:SO4201 3.3 91.2 1.0 CA O:CA401 3.3 46.6 1.0 N O:SER184 3.5 38.8 1.0 O3 N:SO4201 3.5 73.2 1.0 OG O:SER182 3.5 50.2 1.0 CB O:SER184 3.7 43.2 1.0 CB O:SER182 3.8 44.8 1.0 O1 N:SO4201 3.9 68.2 1.0 N O:ASN183 3.9 41.7 1.0 O O:GLY247 4.0 42.0 1.0 CA O:SER184 4.1 37.8 1.0 C O:ASN183 4.4 40.7 1.0 CB O:ASN183 4.4 42.3 1.0 O2 N:SO4201 4.5 72.5 1.0 CA O:ASN183 4.5 41.2 1.0 C O:SER182 4.6 45.5 1.0 CA O:ASP248 4.7 39.3 1.0 CA O:SER182 4.8 46.3 1.0 C O:ASP248 5.0 42.9 1.0

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