Cobalt in PDB 6ndb: Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt

The structure of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt, PDB code: 6ndb 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)	47.07 / 3.20
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	131.836, 131.836, 251.702, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 29.2

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

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

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

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ C:Co401 b:63.6 occ:1.00 OG C:SER184 2.0 50.3 1.0 OD1 C:ASP283 2.2 60.0 1.0 OG C:SER182 2.7 47.0 1.0 CG C:ASP283 3.0 62.1 1.0 CB C:SER184 3.2 51.5 1.0 OD2 C:ASP283 3.2 56.5 1.0 O4 B:SO4201 3.4 0.4 1.0 NA C:NA402 3.4 35.8 1.0 O3 B:SO4201 3.4 74.7 1.0 OD2 C:ASP180 3.7 51.2 1.0 OG1 C:THR250 3.8 63.3 1.0 S B:SO4201 3.9 0.6 1.0 CB C:SER182 3.9 42.1 1.0 O C:ASP283 3.9 52.5 1.0 C C:ASP283 4.2 53.2 1.0 O1 B:SO4201 4.2 65.0 1.0 CA C:GLY284 4.3 48.9 1.0 CA C:SER184 4.4 55.8 1.0 CB C:ASP283 4.4 56.8 1.0 N C:SER184 4.4 59.1 1.0 N C:GLY284 4.5 46.5 1.0 CG C:ASP180 4.5 59.7 1.0 OD1 C:ASP180 4.6 65.6 1.0 CA C:ASP283 4.8 51.1 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ F:Co401 b:63.2 occ:1.00 OG F:SER184 2.4 57.1 1.0 OD1 F:ASP283 2.5 61.8 1.0 OG F:SER182 2.6 25.6 1.0 O4 E:SO4203 2.6 85.0 1.0 NA F:NA402 3.3 21.1 1.0 OD2 F:ASP180 3.5 39.9 1.0 S E:SO4203 3.5 98.7 1.0 O3 E:SO4203 3.6 83.4 1.0 CB F:SER184 3.6 46.0 1.0 CB F:SER182 3.7 30.9 1.0 CG F:ASP283 3.7 57.1 1.0 OG1 F:THR250 3.8 54.8 1.0 O F:ASP283 4.0 43.0 1.0 O2 E:SO4203 4.0 68.1 1.0 C F:ASP283 4.1 46.3 1.0 CA F:GLY284 4.2 51.8 1.0 N F:GLY284 4.3 46.5 1.0 OD2 F:ASP283 4.3 57.1 1.0 CG F:ASP180 4.4 44.1 1.0 OD1 F:ASP180 4.5 43.1 1.0 O1 E:SO4203 4.8 72.9 1.0 CB F:ASP283 4.8 53.5 1.0 CA F:SER184 4.8 44.6 1.0 CA F:ASP283 4.8 47.6 1.0 N F:SER184 4.9 48.3 1.0 CG2 F:THR250 4.9 64.8 1.0 CA F:SER182 4.9 35.3 1.0 CB F:THR250 5.0 58.3 1.0 N F:ASP283 5.0 43.9 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ I:Co401 b:60.1 occ:1.00 OG I:SER184 2.4 70.2 1.0 O4 H:SO4202 2.5 0.4 1.0 OD1 I:ASP283 2.6 57.8 1.0 OG I:SER182 2.7 24.6 1.0 NA I:NA402 3.3 24.2 1.0 S H:SO4202 3.5 0.1 1.0 OD2 I:ASP180 3.5 35.5 1.0 O3 H:SO4202 3.6 97.1 1.0 CB I:SER184 3.6 51.2 1.0 OG1 I:THR250 3.6 58.4 1.0 CG I:ASP283 3.7 62.4 1.0 CB I:SER182 3.8 29.3 1.0 O I:ASP283 3.9 40.7 1.0 C I:ASP283 4.0 48.2 1.0 O2 H:SO4202 4.0 66.0 1.0 CA I:GLY284 4.1 53.7 1.0 N I:GLY284 4.2 49.0 1.0 OD2 I:ASP283 4.4 64.7 1.0 CG I:ASP180 4.5 37.3 1.0 OD1 I:ASP180 4.6 34.2 1.0 O1 H:SO4202 4.7 77.9 1.0 CA I:ASP283 4.8 50.0 1.0 CB I:ASP283 4.8 56.2 1.0 CA I:SER184 4.8 49.2 1.0 CB I:THR250 4.9 63.3 1.0 N I:SER184 4.9 51.7 1.0 CG2 I:THR250 4.9 70.5 1.0 N I:ASP283 4.9 44.0 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ L:Co401 b:63.0 occ:1.00 OG L:SER184 2.0 41.4 1.0 OD1 L:ASP283 2.2 57.4 1.0 OG L:SER182 2.7 48.4 1.0 CG L:ASP283 3.1 56.7 1.0 CB L:SER184 3.2 42.8 1.0 OD2 L:ASP283 3.3 59.6 1.0 NA L:NA402 3.3 28.5 1.0 O3 K:SO4202 3.4 76.9 1.0 O4 K:SO4202 3.4 97.4 1.0 OG1 L:THR250 3.8 55.2 1.0 S K:SO4202 3.8 99.6 1.0 O L:ASP283 3.9 53.1 1.0 OD2 L:ASP180 3.9 49.9 1.0 CB L:SER182 3.9 42.3 1.0 O1 K:SO4202 4.0 75.4 1.0 C L:ASP283 4.2 57.6 1.0 CA L:GLY284 4.3 52.0 1.0 CA L:SER184 4.4 48.0 1.0 N L:SER184 4.4 55.7 1.0 CB L:ASP283 4.5 53.7 1.0 N L:GLY284 4.5 51.8 1.0 CG L:ASP180 4.7 56.0 1.0 OD1 L:ASP180 4.7 63.7 1.0 CA L:ASP283 4.8 50.5 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ O:Co401 b:89.4 occ:1.00 OG O:SER184 2.1 53.7 1.0 OD1 O:ASP283 2.4 51.0 1.0 OG O:SER182 2.6 71.3 1.0 O4 N:SO4201 2.8 99.8 1.0 CB O:SER184 3.2 68.0 1.0 CG O:ASP283 3.4 54.6 1.0 OG1 O:THR250 3.6 37.1 1.0 NA O:NA402 3.6 49.7 1.0 OD2 O:ASP180 3.7 52.3 1.0 OD2 O:ASP283 3.8 70.1 1.0 CB O:SER182 3.8 61.7 1.0 S N:SO4201 3.9 0.3 1.0 O2 N:SO4201 4.1 0.8 1.0 O O:ASP283 4.2 77.9 1.0 CA O:GLY284 4.3 56.6 1.0 C O:ASP283 4.4 58.2 1.0 O1 N:SO4201 4.4 99.0 1.0 CA O:SER184 4.4 60.4 1.0 OD1 O:ASP180 4.5 72.4 1.0 CG O:ASP180 4.5 59.4 1.0 N O:GLY284 4.5 49.7 1.0 N O:SER184 4.6 57.7 1.0 CB O:ASP283 4.7 53.4 1.0 CB O:THR250 5.0 37.9 1.0 CA O:ASP283 5.0 54.0 1.0 CA O:SER182 5.0 59.4 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain and Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ R:Co401 b:88.3 occ:1.00 OG R:SER184 2.0 51.3 1.0 OD1 R:ASP283 2.4 50.6 1.0 OG R:SER182 2.7 62.8 1.0 CB R:SER184 3.1 57.1 1.0 O3 Q:SO4202 3.3 96.2 1.0 CG R:ASP283 3.5 54.2 1.0 NA R:NA404 3.6 50.5 1.0 O4 Q:SO4202 3.6 0.8 1.0 OG1 R:THR250 3.7 39.5 1.0 OD2 R:ASP180 3.7 60.8 1.0 O R:ASP283 3.7 76.2 1.0 CB R:SER182 3.9 56.9 1.0 OD2 R:ASP283 3.9 65.5 1.0 S Q:SO4202 4.0 0.8 1.0 C R:ASP283 4.2 54.2 1.0 CA R:GLY284 4.3 56.2 1.0 CA R:SER184 4.4 54.2 1.0 O1 Q:SO4202 4.5 0.5 1.0 N R:SER184 4.5 49.5 1.0 OD1 R:ASP180 4.5 76.0 1.0 CG R:ASP180 4.5 63.7 1.0 N R:GLY284 4.5 50.5 1.0 CB R:ASP283 4.8 50.3 1.0 CA R:ASP283 4.9 49.3 1.0

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