Calcium 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
Sodium	(Na)	5 atoms

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium, PDB code: 6nd9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca401 b:45.9 occ:1.00 OG C:SER184 1.9 30.4 1.0 OD1 C:ASP283 2.1 33.2 1.0 OG C:SER182 2.6 31.7 1.0 O4 C:SO4402 2.9 0.1 1.0 O3 C:SO4402 3.1 60.5 1.0 CB C:SER184 3.1 30.0 1.0 CG C:ASP283 3.1 38.4 1.0 NA C:NA403 3.4 28.6 1.0 S C:SO4402 3.5 91.6 1.0 OD2 C:ASP283 3.5 38.0 1.0 O C:ASP283 3.8 33.0 1.0 OD2 C:ASP180 3.8 48.5 1.0 OG1 C:THR250 3.8 41.1 1.0 CB C:SER182 3.8 35.1 1.0 O1 C:SO4402 3.9 52.6 1.0 C C:ASP283 4.1 33.5 1.0 CA C:GLY284 4.3 37.9 1.0 N C:GLY284 4.4 33.9 1.0 CA C:SER184 4.4 37.5 1.0 CB C:ASP283 4.5 38.7 1.0 N C:SER184 4.5 44.0 1.0 CG C:ASP180 4.6 45.3 1.0 OD1 C:ASP180 4.6 47.4 1.0 CA C:ASP283 4.7 33.3 1.0 O2 C:SO4402 4.8 47.1 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca401 b:33.4 occ:1.00 OG F:SER184 2.2 30.4 1.0 O4 E:SO4203 2.3 96.5 1.0 OD1 F:ASP283 2.3 49.0 1.0 OG F:SER182 2.4 25.7 1.0 NA F:NA402 3.3 21.2 1.0 CG F:ASP283 3.4 38.1 1.0 CB F:SER184 3.4 27.8 1.0 S E:SO4203 3.4 91.0 1.0 O3 E:SO4203 3.5 65.6 1.0 OD2 F:ASP180 3.6 40.8 1.0 CB F:SER182 3.6 30.5 1.0 OG1 F:THR250 3.6 32.0 1.0 OD2 F:ASP283 3.9 42.3 1.0 O F:ASP283 4.1 31.0 1.0 C F:ASP283 4.2 30.5 1.0 O2 E:SO4203 4.2 46.2 1.0 CA F:GLY284 4.3 31.3 1.0 N F:GLY284 4.4 29.5 1.0 OD1 F:ASP180 4.4 41.5 1.0 CG F:ASP180 4.4 36.9 1.0 O1 E:SO4203 4.5 51.1 1.0 CA F:SER184 4.6 28.9 1.0 N F:SER184 4.6 38.1 1.0 CB F:ASP283 4.7 38.0 1.0 CA F:SER182 4.9 27.9 1.0 CA F:ASP283 4.9 34.1 1.0 CB F:THR250 5.0 35.1 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca401 b:34.3 occ:1.00 OG I:SER184 2.1 36.8 1.0 OD1 I:ASP283 2.3 51.5 1.0 O4 H:SO4202 2.3 83.7 1.0 OG I:SER182 2.4 27.0 1.0 NA I:NA402 3.2 26.9 1.0 CB I:SER184 3.4 30.3 1.0 CG I:ASP283 3.4 40.9 1.0 S H:SO4202 3.4 94.9 1.0 O3 H:SO4202 3.5 68.0 1.0 CB I:SER182 3.6 29.5 1.0 OD2 I:ASP180 3.6 38.6 1.0 OG1 I:THR250 3.6 40.5 1.0 OD2 I:ASP283 3.9 39.8 1.0 O I:ASP283 4.1 34.7 1.0 O2 H:SO4202 4.1 47.1 1.0 C I:ASP283 4.2 34.6 1.0 CA I:GLY284 4.3 35.6 1.0 N I:GLY284 4.4 34.9 1.0 OD1 I:ASP180 4.4 39.0 1.0 CG I:ASP180 4.4 36.6 1.0 CA I:SER184 4.5 30.2 1.0 O1 H:SO4202 4.6 51.6 1.0 N I:SER184 4.6 39.1 1.0 CB I:ASP283 4.7 41.2 1.0 CA I:SER182 4.9 26.0 1.0 CA I:ASP283 4.9 37.0 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca401 b:43.7 occ:1.00 OG L:SER184 1.9 33.0 1.0 OD1 L:ASP283 2.1 33.4 1.0 OG L:SER182 2.6 34.4 1.0 CG L:ASP283 3.1 35.6 1.0 CB L:SER184 3.1 30.7 1.0 O3 L:SO4402 3.2 59.0 1.0 NA L:NA403 3.3 26.7 1.0 O4 L:SO4402 3.4 86.1 1.0 OD2 L:ASP283 3.5 37.7 1.0 S L:SO4402 3.7 92.5 1.0 O L:ASP283 3.8 31.9 1.0 OD2 L:ASP180 3.8 47.2 1.0 O1 L:SO4402 3.8 60.9 1.0 CB L:SER182 3.8 35.4 1.0 OG1 L:THR250 3.9 39.9 1.0 C L:ASP283 4.1 34.6 1.0 CA L:GLY284 4.3 38.2 1.0 CA L:SER184 4.4 36.6 1.0 N L:GLY284 4.4 34.1 1.0 CB L:ASP283 4.4 37.9 1.0 N L:SER184 4.5 44.2 1.0 CG L:ASP180 4.6 45.8 1.0 OD1 L:ASP180 4.6 48.3 1.0 CA L:ASP283 4.7 34.7 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca401 b:46.6 occ:1.00 OG O:SER184 2.0 40.7 1.0 OD1 O:ASP283 2.3 34.4 1.0 OG O:SER182 2.5 50.2 1.0 O4 N:SO4201 2.7 72.6 1.0 CB O:SER184 3.3 43.2 1.0 NA O:NA402 3.3 26.6 1.0 CG O:ASP283 3.3 37.1 1.0 OG1 O:THR250 3.6 33.9 1.0 CB O:SER182 3.7 44.8 1.0 OD2 O:ASP180 3.7 49.7 1.0 OD2 O:ASP283 3.8 53.3 1.0 S N:SO4201 3.9 91.2 1.0 O O:ASP283 4.0 58.1 1.0 C O:ASP283 4.1 45.1 1.0 CA O:GLY284 4.2 48.6 1.0 O2 N:SO4201 4.3 72.5 1.0 O1 N:SO4201 4.3 68.2 1.0 N O:GLY284 4.3 42.9 1.0 OD1 O:ASP180 4.5 47.6 1.0 CG O:ASP180 4.5 41.5 1.0 CA O:SER184 4.5 37.8 1.0 N O:SER184 4.6 38.8 1.0 CB O:ASP283 4.6 33.3 1.0 CA O:ASP283 4.8 39.4 1.0 CA O:SER182 5.0 46.3 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Rhodocetin in Complex with the Integrin ALPHA2-A Domain with Calcium within 5.0Å range: probe atom residue distance (Å) B Occ R:Ca401 b:56.1 occ:1.00 OG R:SER184 2.0 40.3 1.0 OD1 R:ASP283 2.3 39.3 1.0 OG R:SER182 2.5 44.0 1.0 O4 Q:SO4202 2.8 0.2 1.0 O3 Q:SO4202 3.1 55.2 1.0 CB R:SER184 3.3 43.4 1.0 CG R:ASP283 3.4 39.9 1.0 S Q:SO4202 3.5 99.4 1.0 OG1 R:THR250 3.6 34.9 1.0 CB R:SER182 3.6 38.2 1.0 OD2 R:ASP180 3.7 48.1 1.0 OD2 R:ASP283 3.8 51.8 1.0 O R:ASP283 4.1 56.2 1.0 O1 Q:SO4202 4.2 62.7 1.0 C R:ASP283 4.2 45.6 1.0 CA R:GLY284 4.2 46.5 1.0 N R:GLY284 4.4 41.2 1.0 OD1 R:ASP180 4.5 42.0 1.0 CG R:ASP180 4.5 37.9 1.0 CA R:SER184 4.5 36.8 1.0 N R:SER184 4.5 41.0 1.0 CB R:ASP283 4.7 33.5 1.0 O2 Q:SO4202 4.7 57.2 1.0 CA R:ASP283 4.9 39.6 1.0 CA R:SER182 4.9 40.0 1.0

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