Sodium in PDB 6ndc: Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound, PDB code: 6ndc 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)	92.90 / 3.35
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	131.140, 131.140, 251.460, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 27.6

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

Chromium	(Cr)	6 atoms
Chlorine	(Cl)	9 atoms

The binding sites of Sodium atom in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Chromium Bound (pdb code 6ndc). 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 with Chromium Bound, PDB code: 6ndc:
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 with Chromium Bound


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 Chromium Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:31.6 occ:1.00 O3 C:SO4402 2.6 82.3 1.0 N C:SER184 3.1 41.1 1.0 N C:ASN183 3.5 40.4 1.0 OG C:SER184 3.6 47.2 1.0 CB C:ASN183 3.7 36.8 1.0 C C:ASN183 3.7 41.6 1.0 CA C:ASN183 3.8 39.5 1.0 CB C:SER184 3.8 42.0 1.0 CR C:CR401 3.9 52.6 1.0 CA C:SER184 3.9 40.6 1.0 O C:GLY247 3.9 33.3 1.0 S C:SO4402 3.9 96.2 1.0 CB C:SER182 4.1 39.1 1.0 OG C:SER182 4.2 35.3 1.0 CG C:ASN183 4.4 35.2 1.0 O1 C:SO4402 4.4 78.5 1.0 C C:SER182 4.5 44.3 1.0 ND2 C:ASN183 4.6 38.9 1.0 O4 C:SO4402 4.6 0.3 1.0 CA C:ASP248 4.7 39.3 1.0 O C:ASN183 4.8 42.4 1.0 O2 C:SO4402 4.8 72.8 1.0 CA C:SER182 4.9 40.3 1.0 C C:GLY247 4.9 33.8 1.0

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


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 Chromium Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Na403 b:5.7 occ:1.00 O3 E:SO4202 2.0 79.9 1.0 OG F:SER184 2.9 27.3 1.0 S E:SO4202 3.4 89.0 1.0 OG F:SER182 3.5 28.6 1.0 CR F:CR402 3.6 47.4 1.0 N F:SER184 3.6 31.3 1.0 CB F:SER182 3.7 30.1 1.0 N F:ASN183 3.8 31.5 1.0 O4 E:SO4202 3.9 81.6 1.0 O F:GLY247 3.9 29.5 1.0 CB F:SER184 3.9 27.3 1.0 O2 E:SO4202 4.0 70.0 1.0 CB F:ASN183 4.3 31.8 1.0 O1 E:SO4202 4.3 62.0 1.0 CA F:SER184 4.3 28.7 1.0 CA F:ASP248 4.4 27.9 1.0 CA F:ASN183 4.4 33.2 1.0 C F:ASN183 4.5 35.3 1.0 C F:SER182 4.5 30.9 1.0 CA F:SER182 4.6 30.2 1.0 C F:ASP248 4.9 28.1 1.0 C F:GLY247 4.9 29.8 1.0

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


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 Chromium Bound within 5.0Å range: probe atom residue distance (Å) B Occ I:Na403 b:9.0 occ:1.00 O3 H:SO4201 2.0 69.8 1.0 OG I:SER184 2.8 26.4 1.0 S H:SO4201 3.3 81.2 1.0 OG I:SER182 3.4 20.7 1.0 CR I:CR402 3.5 44.2 1.0 N I:SER184 3.6 31.3 1.0 O4 H:SO4201 3.6 70.5 1.0 CB I:SER182 3.7 22.6 1.0 N I:ASN183 3.8 28.2 1.0 CB I:SER184 3.8 27.1 1.0 O I:GLY247 4.0 31.6 1.0 O2 H:SO4201 4.0 57.5 1.0 O1 H:SO4201 4.2 61.2 1.0 CB I:ASN183 4.3 32.7 1.0 CA I:SER184 4.3 28.2 1.0 CA I:ASP248 4.3 28.6 1.0 CA I:ASN183 4.4 31.3 1.0 C I:ASN183 4.5 32.2 1.0 C I:SER182 4.5 25.1 1.0 CA I:SER182 4.7 23.6 1.0 C I:ASP248 4.7 28.4 1.0 O I:ASP248 4.9 28.1 1.0 C I:GLY247 4.9 31.7 1.0

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


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 Chromium Bound within 5.0Å range: probe atom residue distance (Å) B Occ L:Na402 b:38.1 occ:1.00 O3 K:SO4202 2.0 84.7 1.0 CR L:CR401 3.0 53.6 1.0 OG L:SER184 3.1 32.5 1.0 S K:SO4202 3.3 0.6 1.0 N L:SER184 3.5 35.5 1.0 CB L:SER184 3.7 30.2 1.0 OG L:SER182 3.7 44.0 1.0 O1 K:SO4202 3.8 93.9 1.0 N L:ASN183 3.8 38.0 1.0 CB L:SER182 3.9 43.7 1.0 O4 K:SO4202 4.0 1.0 1.0 CA L:SER184 4.1 31.1 1.0 O L:GLY247 4.2 33.9 1.0 O2 K:SO4202 4.3 83.0 1.0 C L:ASN183 4.4 38.5 1.0 CA L:ASN183 4.4 39.4 1.0 CB L:ASN183 4.5 41.9 1.0 C L:SER182 4.6 42.2 1.0 CA L:ASP248 4.7 39.3 1.0 CA L:SER182 4.8 40.9 1.0 C L:ASP248 5.0 40.2 1.0

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


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 Chromium Bound within 5.0Å range: probe atom residue distance (Å) B Occ O:Na402 b:32.0 occ:1.00 O4 N:SO4201 2.4 0.7 1.0 O3 N:SO4201 3.3 84.5 1.0 S N:SO4201 3.4 95.5 1.0 OG O:SER182 3.6 39.7 1.0 O O:GLY247 3.6 49.9 1.0 N O:SER184 3.9 42.1 1.0 OG O:SER184 3.9 43.7 1.0 CR O:CR401 3.9 76.7 1.0 N O:ASN183 3.9 36.1 1.0 CB O:SER182 3.9 39.4 1.0 CB O:SER184 4.1 45.8 1.0 CB O:ASN183 4.2 42.6 1.0 CA O:ASP248 4.3 50.5 1.0 O1 N:SO4201 4.4 89.5 1.0 O2 N:SO4201 4.4 0.2 1.0 CA O:ASN183 4.5 37.7 1.0 CA O:SER184 4.5 44.0 1.0 C O:ASP248 4.6 49.6 1.0 C O:ASN183 4.6 38.0 1.0 C O:GLY247 4.6 47.1 1.0 C O:SER182 4.7 37.6 1.0 O O:ASP248 4.8 48.1 1.0 CG O:ASN183 4.8 45.2 1.0 CA O:SER182 4.9 38.6 1.0 N O:ASP248 5.0 48.9 1.0

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


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 with Chromium Bound within 5.0Å range: probe atom residue distance (Å) B Occ R:Na404 b:35.2 occ:1.00 O3 Q:SO4202 2.1 96.3 1.0 O R:GLY247 3.4 51.9 1.0 OG R:SER182 3.5 45.3 1.0 OG R:SER184 3.5 45.5 1.0 S Q:SO4202 3.5 0.4 1.0 N R:ASN183 3.7 35.9 1.0 CR R:CR401 3.7 76.3 1.0 N R:SER184 3.8 37.7 1.0 CB R:SER182 3.8 44.1 1.0 CB R:SER184 4.0 45.9 1.0 O4 Q:SO4202 4.1 0.3 1.0 CB R:ASN183 4.1 40.5 1.0 CA R:ASP248 4.2 49.7 1.0 O1 Q:SO4202 4.3 90.1 1.0 CA R:ASN183 4.3 37.1 1.0 O2 Q:SO4202 4.3 0.5 1.0 O R:ASP248 4.4 48.8 1.0 C R:ASP248 4.4 47.5 1.0 C R:ASN183 4.5 35.3 1.0 C R:GLY247 4.5 51.5 1.0 C R:SER182 4.5 39.4 1.0 CA R:SER184 4.5 41.4 1.0 CA R:SER182 4.7 43.9 1.0 CG R:ASN183 4.8 45.0 1.0 N R:ASP248 4.8 52.4 1.0

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