Calcium in PDB 7f9g: Thrombocorticin in Complex with CA2+ and Fucose

The structure of Thrombocorticin in Complex with CA2+ and Fucose, PDB code: 7f9g was solved by H.Kageyama, K.Onodera, R.Sakai, Y.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.43 / 1.33
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.52, 44.72, 108.58, 90, 90, 90
R / Rfree (%)	15.5 / 16.8

The binding sites of Calcium atom in the Thrombocorticin in Complex with CA2+ and Fucose (pdb code 7f9g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Thrombocorticin in Complex with CA2+ and Fucose, PDB code: 7f9g:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Thrombocorticin in Complex with CA2+ and Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Thrombocorticin in Complex with CA2+ and Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:5.9 occ:1.00 OD1 A:ASP121 2.3 5.7 1.0 OD1 A:ASN120 2.4 6.2 1.0 O A:GLN26 2.4 6.7 1.0 OD2 A:ASP118 2.4 6.9 1.0 OXT B:GLY132 2.4 6.2 1.0 O4 A:FUC201 2.5 6.7 1.0 O3 A:FUC201 2.5 6.5 1.0 CG A:ASP118 3.1 6.1 1.0 OD1 A:ASP118 3.2 7.5 1.0 CG A:ASN120 3.4 5.5 1.0 C3 A:FUC201 3.4 8.2 1.0 C B:GLY132 3.4 7.8 1.0 C4 A:FUC201 3.4 7.2 1.0 CG A:ASP121 3.5 4.8 1.0 C A:GLN26 3.6 6.6 1.0 O B:GLY132 3.6 8.8 1.0 C2 A:FUC201 3.8 6.8 1.0 ND2 A:ASN120 3.8 5.8 1.0 CA A:CA203 3.9 6.6 1.0 CB A:GLN26 4.2 8.0 1.0 CA A:ASP121 4.2 5.9 1.0 N A:ASP121 4.3 5.4 1.0 OD2 A:ASP121 4.3 6.3 1.0 OD2 A:ASP116 4.4 8.8 1.0 O2 A:FUC201 4.4 7.7 1.0 N A:SER27 4.5 6.7 1.0 CB A:ASP121 4.5 6.3 1.0 O A:HOH342 4.5 8.0 1.0 CA A:SER27 4.5 6.1 1.0 CB A:ASP118 4.5 7.7 1.0 C A:ASN120 4.5 5.8 1.0 CA A:GLN26 4.5 5.3 1.0 CB A:SER27 4.7 7.4 1.0 C5 A:FUC201 4.7 8.7 1.0 CB A:ASN120 4.7 5.3 1.0 CA B:GLY132 4.7 9.0 1.0 O A:ASN120 4.8 6.0 1.0 OD1 A:ASP116 4.9 8.7 1.0 N A:ASN120 5.0 5.6 1.0 CA A:ASN120 5.0 5.0 1.0 O5 A:FUC201 5.0 9.3 1.0

Calcium binding site 2 out of 4 in the Thrombocorticin in Complex with CA2+ and Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Thrombocorticin in Complex with CA2+ and Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:6.6 occ:1.00 OD1 A:ASP118 2.4 7.5 1.0 OD2 A:ASP121 2.4 6.3 1.0 O A:HOH374 2.4 8.0 1.0 OD1 A:ASP116 2.4 8.7 1.0 O3 A:FUC201 2.5 6.5 1.0 OD1 A:ASN108 2.5 6.0 1.0 O2 A:FUC201 2.6 7.7 1.0 OD1 A:ASP121 2.9 5.7 1.0 CG A:ASP121 3.0 4.8 1.0 CG A:ASP118 3.4 6.1 1.0 C3 A:FUC201 3.4 8.2 1.0 CG A:ASP116 3.4 7.0 1.0 C2 A:FUC201 3.4 6.8 1.0 CG A:ASN108 3.6 6.4 1.0 OD2 A:ASP116 3.7 8.8 1.0 OD2 A:ASP118 3.8 6.9 1.0 CA A:CA202 3.9 5.9 1.0 N A:ASP118 4.2 8.2 1.0 ND2 A:ASN108 4.2 6.7 1.0 N A:ASP109 4.2 5.7 1.0 O A:HOH430 4.3 25.1 1.0 CB A:ASP121 4.5 6.3 1.0 CA A:ASN108 4.5 5.8 1.0 OD2 A:ASP109 4.5 7.0 1.0 CB A:ASP118 4.6 7.7 1.0 CB A:ASN108 4.6 6.0 1.0 N A:ARG117 4.7 7.4 1.0 CB A:ASP109 4.7 7.0 1.0 N A:PHE119 4.7 6.2 1.0 C4 A:FUC201 4.8 7.2 1.0 C A:ASN108 4.8 6.0 1.0 O A:HOH435 4.8 16.1 1.0 CA A:ASP118 4.8 6.5 1.0 CB A:ASP116 4.8 8.7 1.0 O A:ASP109 4.9 7.8 1.0 C1 A:FUC201 4.9 11.1 1.0 CG A:ASP109 4.9 6.8 1.0 N A:ASP116 4.9 8.3 1.0 OD1 A:ASN120 4.9 6.2 1.0 O4 A:FUC201 5.0 6.7 1.0

Calcium binding site 3 out of 4 in the Thrombocorticin in Complex with CA2+ and Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Thrombocorticin in Complex with CA2+ and Fucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:11.2 occ:1.00 OD1 B:ASP121 2.3 11.3 1.0 OD1 B:ASN120 2.4 9.9 1.0 OXT A:GLY132 2.4 13.9 1.0 O B:GLN26 2.4 11.0 1.0 OD2 B:ASP118 2.5 12.9 0.5 O4 B:FUC201 2.5 15.4 1.0 O3 B:FUC201 2.7 23.5 1.0 C A:GLY132 3.4 19.7 1.0 CG B:ASP118 3.4 8.9 0.5 CG B:ASN120 3.4 8.1 1.0 C3 B:FUC201 3.5 22.8 1.0 CG B:ASP121 3.5 7.7 1.0 C4 B:FUC201 3.5 28.5 1.0 O A:GLY132 3.6 19.8 1.0 C B:GLN26 3.6 9.3 1.0 OD1 B:ASP118 3.7 12.2 0.5 ND2 B:ASN120 3.8 9.6 1.0 C2 B:FUC201 3.8 16.3 1.0 CA B:CA203 4.1 17.0 1.0 CB B:GLN26 4.1 8.2 1.0 CA B:ASP121 4.1 6.8 1.0 N B:ASP121 4.2 6.5 1.0 OD2 B:ASP121 4.3 9.5 1.0 C B:ASN120 4.4 6.4 1.0 CB B:ASP121 4.4 7.2 1.0 O2 B:FUC201 4.5 17.5 1.0 CA B:GLN26 4.5 7.2 1.0 OD1 B:ASP116 4.6 21.8 1.0 N B:SER27 4.6 9.3 1.0 O B:ASN120 4.6 7.4 1.0 CB B:ASP118 4.6 11.1 0.5 CA B:SER27 4.7 9.8 1.0 OD2 B:ASP118 4.7 13.7 0.5 CA A:GLY132 4.7 22.8 1.0 CB B:SER27 4.7 10.3 1.0 CB B:ASN120 4.7 7.0 1.0 CB B:ASP118 4.7 10.9 0.5 C5 B:FUC201 4.8 29.7 1.0 CA B:ASN120 5.0 7.1 1.0

Calcium binding site 4 out of 4 in the Thrombocorticin in Complex with CA2+ and Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Thrombocorticin in Complex with CA2+ and Fucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:17.0 occ:1.00 OD2 B:ASP116 2.3 20.5 1.0 OD2 B:ASP121 2.3 9.5 1.0 O B:HOH354 2.4 14.1 1.0 OD1 B:ASP118 2.4 12.2 0.5 O2 B:FUC201 2.6 17.5 1.0 O3 B:FUC201 2.7 23.5 1.0 OD1 B:ASN108 2.7 12.7 1.0 OD1 B:ASP121 2.9 11.3 1.0 CG B:ASP121 3.0 7.7 1.0 CG B:ASP118 3.3 8.9 0.5 CG B:ASP116 3.4 19.8 1.0 C2 B:FUC201 3.4 16.3 1.0 C3 B:FUC201 3.5 22.8 1.0 OD2 B:ASP118 3.6 12.9 0.5 OD1 B:ASP116 3.8 21.8 1.0 CG B:ASN108 3.8 9.1 1.0 CA B:CA202 4.1 11.2 1.0 N B:ASP109 4.2 7.0 1.0 N B:ASP118 4.3 10.3 0.5 N B:ARG117 4.4 12.4 0.5 N B:ARG117 4.4 12.4 0.5 N B:ASP116 4.4 25.3 1.0 N B:ASP118 4.4 10.1 0.5 CB B:ASP121 4.5 7.2 1.0 CB B:ASP109 4.5 7.5 1.0 CA B:ASN108 4.5 7.0 1.0 ND2 B:ASN108 4.6 11.4 1.0 CB B:ASP116 4.7 22.9 1.0 CB B:ASN108 4.7 8.2 1.0 CB B:ASP118 4.7 11.1 0.5 O B:HOH422 4.7 26.4 1.0 O B:ASP109 4.7 8.9 1.0 C B:ASN108 4.8 7.5 1.0 CB B:ASP118 4.8 10.9 0.5 OD2 B:ASP109 4.8 12.3 1.0 CA B:ASP116 4.8 21.4 1.0 C B:ASP116 4.8 13.2 1.0 C4 B:FUC201 4.9 28.5 1.0 C1 B:FUC201 4.9 25.2 1.0 CG B:ASP109 4.9 8.4 1.0 CA B:ASP109 4.9 7.8 1.0 N B:PHE119 4.9 8.0 1.0 OD1 B:ASN120 4.9 9.9 1.0

H.Kageyama, K.Onodera, R.Sakai, Y.Tanaka. Crystal Structure of Thrombocorticin in Complex with CA2+ and Fucose To Be Published.