Cadmium in PDB 6nda: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium, PDB code: 6nda 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)	92.47 / 3.15
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	130.530, 130.530, 250.919, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 27.1

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

Chlorine	(Cl)	9 atoms
Sodium	(Na)	6 atoms

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

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


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd401 b:40.0 occ:1.00 OG C:SER184 1.8 31.9 1.0 OD1 C:ASP283 2.2 27.3 1.0 OG C:SER182 2.5 42.1 1.0 CG C:ASP283 2.8 33.8 1.0 OD2 C:ASP283 2.9 36.5 1.0 CB C:SER184 2.9 33.1 1.0 NA C:NA403 2.9 8.1 1.0 O2 C:SO4402 3.1 57.7 1.0 O4 C:SO4402 3.1 96.8 1.0 OD2 C:ASP180 3.5 34.4 1.0 S C:SO4402 3.6 83.2 1.0 O C:ASP283 3.6 39.0 1.0 CB C:SER182 3.7 36.3 1.0 OG1 C:THR250 3.8 52.9 1.0 O1 C:SO4402 4.0 59.9 1.0 C C:ASP283 4.1 35.4 1.0 CA C:SER184 4.1 35.0 1.0 CB C:ASP283 4.3 37.1 1.0 N C:SER184 4.3 37.2 1.0 CG C:ASP180 4.4 39.8 1.0 CA C:GLY284 4.5 37.4 1.0 OD1 C:ASP180 4.5 50.6 1.0 N C:GLY284 4.6 31.3 1.0 CA C:ASP283 4.8 35.5 1.0 CA C:SER182 4.9 34.6 1.0 O3 C:SO4402 4.9 47.3 1.0 C C:SER184 5.0 37.0 1.0

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


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ F:Cd401 b:35.7 occ:1.00 OG F:SER184 2.0 39.5 1.0 OG F:SER182 2.2 14.4 1.0 OD1 F:ASP283 2.3 55.0 1.0 O2 F:SO4402 2.4 56.4 1.0 NA F:NA403 3.0 19.3 1.0 CB F:SER184 3.2 36.9 1.0 CB F:SER182 3.3 19.3 1.0 CG F:ASP283 3.4 56.4 1.0 S F:SO4402 3.5 83.4 1.0 OD2 F:ASP180 3.6 32.0 1.0 O3 F:SO4402 3.6 85.0 1.0 O F:ASP283 3.8 33.4 1.0 O4 F:SO4402 4.0 48.0 1.0 OD2 F:ASP283 4.0 79.0 1.0 OG1 F:THR250 4.0 33.9 1.0 C F:ASP283 4.1 37.6 1.0 CG F:ASP180 4.4 31.3 1.0 OD1 F:ASP180 4.4 31.0 1.0 CA F:GLY284 4.4 43.9 1.0 CA F:SER184 4.4 34.8 1.0 N F:GLY284 4.5 37.6 1.0 N F:SER184 4.5 38.5 1.0 CB F:ASP283 4.6 48.3 1.0 CA F:SER182 4.6 20.9 1.0 CA F:ASP283 4.7 40.0 1.0 O1 F:SO4402 4.7 52.5 1.0 N F:ASP283 5.0 35.7 1.0 C F:SER182 5.0 22.8 1.0

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


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ I:Cd401 b:33.9 occ:1.00 OG I:SER184 1.9 37.0 1.0 OG I:SER182 2.2 20.8 1.0 OD1 I:ASP283 2.3 43.4 1.0 O1 H:SO4202 2.5 57.3 1.0 CB I:SER184 3.2 36.2 1.0 CB I:SER182 3.3 24.3 1.0 NA I:NA402 3.3 13.9 1.0 OD2 I:ASP180 3.4 24.5 1.0 S H:SO4202 3.4 85.8 1.0 O3 H:SO4202 3.5 82.9 1.0 CG I:ASP283 3.5 49.4 1.0 O2 H:SO4202 3.9 51.0 1.0 O I:ASP283 3.9 35.8 1.0 OG1 I:THR250 4.1 32.7 1.0 C I:ASP283 4.1 40.1 1.0 OD2 I:ASP283 4.2 63.7 1.0 CA I:SER184 4.3 36.5 1.0 CG I:ASP180 4.3 26.0 1.0 N I:SER184 4.3 42.0 1.0 OD1 I:ASP180 4.4 24.1 1.0 N I:GLY284 4.5 38.3 1.0 CA I:GLY284 4.5 42.7 1.0 CA I:SER182 4.6 24.2 1.0 CB I:ASP283 4.6 49.1 1.0 O4 H:SO4202 4.7 62.1 1.0 CA I:ASP283 4.8 42.9 1.0 C I:SER182 4.9 26.8 1.0 N I:ASN183 5.0 33.5 1.0

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


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd401 b:42.7 occ:1.00 OG L:SER184 1.8 23.9 1.0 OD1 L:ASP283 2.1 25.3 1.0 OG L:SER182 2.5 41.2 1.0 CG L:ASP283 2.7 32.3 1.0 NA L:NA402 2.7 14.7 1.0 OD2 L:ASP283 2.8 29.6 1.0 CB L:SER184 2.8 27.5 1.0 O1 K:SO4202 2.9 90.7 1.0 O3 K:SO4202 3.5 75.1 1.0 O L:ASP283 3.5 34.3 1.0 CB L:SER182 3.6 35.6 1.0 OD2 L:ASP180 3.6 37.0 1.0 S K:SO4202 3.7 91.3 1.0 OG1 L:THR250 3.9 45.1 1.0 O4 K:SO4202 4.0 64.1 1.0 C L:ASP283 4.1 37.4 1.0 CA L:SER184 4.1 29.3 1.0 CB L:ASP283 4.2 35.0 1.0 N L:SER184 4.4 32.7 1.0 CA L:GLY284 4.4 38.5 1.0 CG L:ASP180 4.5 42.4 1.0 OD1 L:ASP180 4.6 49.1 1.0 N L:GLY284 4.6 35.8 1.0 CA L:ASP283 4.7 32.6 1.0 C L:SER184 4.9 30.9 1.0 CA L:SER182 4.9 32.8 1.0 N L:ILE185 4.9 38.3 1.0

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


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ O:Cd401 b:45.2 occ:1.00 OG O:SER184 1.9 21.0 1.0 OD1 O:ASP283 2.2 32.6 1.0 OG O:SER182 2.4 53.3 1.0 O1 N:SO4201 2.6 86.7 1.0 NA O:NA402 3.0 19.1 1.0 CB O:SER184 3.0 31.0 1.0 CG O:ASP283 3.1 36.6 1.0 OD2 O:ASP283 3.3 37.7 1.0 OG1 O:THR250 3.5 26.0 1.0 CB O:SER182 3.6 48.9 1.0 OD2 O:ASP180 3.7 46.8 1.0 S N:SO4201 3.9 99.0 1.0 CA O:SER184 4.2 34.4 1.0 CA O:GLY284 4.3 57.3 1.0 N O:SER184 4.3 33.5 1.0 OD1 O:ASP180 4.3 46.0 1.0 O2 N:SO4201 4.4 85.0 1.0 C O:ASP283 4.4 50.7 1.0 CG O:ASP180 4.4 44.7 1.0 O4 N:SO4201 4.4 63.4 1.0 O O:ASP283 4.4 60.8 1.0 N O:GLY284 4.5 54.8 1.0 CB O:ASP283 4.5 36.4 1.0 CA O:SER182 4.8 48.5 1.0 CB O:THR250 4.9 27.7 1.0 CA O:ASP283 4.9 38.7 1.0 C O:SER182 4.9 42.9 1.0 O3 N:SO4201 5.0 76.6 1.0

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


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ R:Cd401 b:45.9 occ:1.00 OG R:SER184 1.8 21.9 1.0 OD1 R:ASP283 2.3 26.2 1.0 OG R:SER182 2.4 50.9 1.0 CB R:SER184 3.0 28.4 1.0 NA R:NA404 3.0 11.9 1.0 O3 Q:SO4202 3.2 81.1 1.0 CG R:ASP283 3.3 31.0 1.0 O4 Q:SO4202 3.4 92.0 1.0 OG1 R:THR250 3.5 29.7 1.0 CB R:SER182 3.6 46.3 1.0 OD2 R:ASP283 3.6 38.4 1.0 OD2 R:ASP180 3.7 49.1 1.0 S Q:SO4202 3.8 98.0 1.0 O R:ASP283 3.9 65.4 1.0 C R:ASP283 4.2 45.8 1.0 CA R:SER184 4.2 31.6 1.0 OD1 R:ASP180 4.2 49.9 1.0 O1 Q:SO4202 4.3 71.2 1.0 CA R:GLY284 4.3 53.0 1.0 N R:SER184 4.3 34.6 1.0 CG R:ASP180 4.3 45.7 1.0 N R:GLY284 4.5 48.1 1.0 CB R:ASP283 4.6 30.9 1.0 CA R:SER182 4.8 45.6 1.0 CA R:ASP283 4.9 34.8 1.0 CB R:THR250 4.9 31.8 1.0

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