Calcium in PDB 7fbl: Thrombocorticin in Complex with CA2+ and Mannose

The structure of Thrombocorticin in Complex with CA2+ and Mannose, PDB code: 7fbl 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)	33.08 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.57, 44.98, 109.26, 90, 90, 90
R / Rfree (%)	16.2 / 18.2

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

Calcium binding site 1 out of 3 in the Thrombocorticin in Complex with CA2+ and Mannose


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 Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:4.9 occ:1.00 HO2 A:MAN201 2.0 7.0 0.6 HO2 A:MAN201 2.0 7.0 0.4 OD1 A:ASP120 2.3 5.0 1.0 OD1 A:ASN119 2.3 4.8 1.0 O A:GLN25 2.4 5.5 1.0 O B:GLY131 2.4 6.3 1.0 OD2 A:ASP117 2.4 5.3 1.0 O3 A:MAN201 2.5 6.7 0.4 O2 A:MAN201 2.5 5.9 0.6 O3 A:MAN201 2.5 6.7 0.6 O2 A:MAN201 2.5 5.9 0.4 CG A:ASP117 3.2 6.4 1.0 HO3 A:MAN201 3.2 8.1 0.4 H4 A:MAN201 3.3 6.6 0.4 OD1 A:ASP117 3.3 6.6 1.0 HO3 A:MAN201 3.3 8.1 0.6 C3 A:MAN201 3.3 7.0 0.4 CG A:ASN119 3.4 4.5 1.0 C3 A:MAN201 3.4 7.0 0.6 C B:GLY131 3.4 8.2 1.0 H4 A:MAN201 3.4 6.5 0.6 C2 A:MAN201 3.4 6.0 0.6 C2 A:MAN201 3.4 6.0 0.4 CG A:ASP120 3.5 4.6 1.0 C A:GLN25 3.6 5.5 1.0 OXT B:GLY131 3.7 7.4 1.0 ND2 A:ASN119 3.7 5.2 1.0 C4 A:MAN201 3.8 5.5 0.4 H2 A:MAN201 3.8 7.1 0.6 H2 A:MAN201 3.8 7.2 0.4 C4 A:MAN201 3.9 5.5 0.6 CA A:CA203 3.9 6.1 1.0 CA A:ASP120 4.2 4.8 1.0 CB A:GLN25 4.2 5.7 1.0 N A:ASP120 4.3 5.1 1.0 H3 A:MAN201 4.3 8.4 0.4 OD2 A:ASP120 4.3 5.2 1.0 H3 A:MAN201 4.3 8.4 0.6 OD2 A:ASP115 4.4 8.5 1.0 O4 A:MAN201 4.4 6.3 0.4 O A:HOH342 4.4 9.8 1.0 CB A:ASP120 4.4 4.6 1.0 N A:SER26 4.5 6.7 1.0 C A:ASN119 4.5 4.9 1.0 O4 A:MAN201 4.5 6.4 0.6 CA A:SER26 4.5 5.9 1.0 CA A:GLN25 4.5 5.0 1.0 CB A:ASP117 4.5 5.8 1.0 CB A:ASN119 4.7 4.0 1.0 CA B:GLY131 4.7 7.6 1.0 O A:ASN119 4.7 5.2 1.0 C1 A:MAN201 4.8 7.4 0.6 C1 A:MAN201 4.8 7.4 0.4 CB A:SER26 4.9 11.8 1.0 HO4 A:MAN201 4.9 7.6 0.4 N A:ASN119 4.9 5.5 1.0 HO4 A:MAN201 4.9 7.7 0.6 OD1 A:ASP115 5.0 8.7 1.0 CA A:ASN119 5.0 4.1 1.0

Calcium binding site 2 out of 3 in the Thrombocorticin in Complex with CA2+ and Mannose


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 Mannose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:6.1 occ:1.00 HO3 A:MAN201 1.9 8.1 0.6 HO3 A:MAN201 2.0 8.1 0.4 OD1 A:ASP117 2.3 6.6 1.0 O A:HOH363 2.4 8.1 1.0 OD2 A:ASP120 2.4 5.2 1.0 OD1 A:ASP115 2.4 8.7 1.0 O3 A:MAN201 2.5 6.7 0.6 OD1 A:ASN107 2.5 5.6 1.0 O3 A:MAN201 2.6 6.7 0.4 O4 A:MAN201 2.6 6.3 0.4 O4 A:MAN201 2.7 6.4 0.6 OD1 A:ASP120 3.0 5.0 1.0 CG A:ASP120 3.0 4.6 1.0 HO4 A:MAN201 3.2 7.6 0.4 HO4 A:MAN201 3.2 7.7 0.6 CG A:ASP117 3.3 6.4 1.0 CG A:ASP115 3.4 8.3 1.0 C3 A:MAN201 3.4 7.0 0.6 C3 A:MAN201 3.4 7.0 0.4 C4 A:MAN201 3.5 5.5 0.4 C4 A:MAN201 3.5 5.5 0.6 CG A:ASN107 3.6 6.2 1.0 H3 A:MAN201 3.6 8.4 0.6 H3 A:MAN201 3.7 8.4 0.4 OD2 A:ASP115 3.7 8.5 1.0 OD2 A:ASP117 3.8 5.3 1.0 H4 A:MAN201 3.8 6.6 0.4 O A:HOH410 3.8 20.1 1.0 H4 A:MAN201 3.8 6.5 0.6 CA A:CA202 3.9 4.9 1.0 N A:ASP108 4.2 5.0 1.0 N A:ASP117 4.2 7.1 1.0 ND2 A:ASN107 4.3 7.0 1.0 CA A:ASN107 4.5 4.8 1.0 OD2 A:ASP108 4.5 9.8 1.0 CB A:ASP120 4.5 4.6 1.0 CB A:ASP117 4.6 5.8 1.0 CB A:ASN107 4.6 4.6 1.0 N A:ARG116 4.6 6.3 1.0 CB A:ASP108 4.7 5.8 1.0 N A:PHE118 4.7 5.3 1.0 O A:HOH431 4.7 25.4 1.0 C A:ASN107 4.8 3.8 1.0 CB A:ASP115 4.8 6.4 1.0 C2 A:MAN201 4.8 6.0 0.6 CA A:ASP117 4.8 4.8 1.0 O A:ASP108 4.8 7.1 1.0 C5 A:MAN201 4.8 6.9 0.4 C2 A:MAN201 4.9 6.0 0.4 N A:ASP115 4.9 8.1 1.0 CG A:ASP108 4.9 7.0 1.0 C5 A:MAN201 4.9 6.8 0.6 HO2 A:MAN201 4.9 7.0 0.6 OD1 A:ASN119 4.9 4.8 1.0 O2 A:MAN201 5.0 5.9 0.6 CA A:ASP108 5.0 5.5 1.0

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


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 Mannose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:13.3 occ:1.00 O B:HOH325 2.3 15.5 1.0 OD1 B:ASP120 2.3 11.5 1.0 O B:GLN25 2.3 11.0 1.0 OXT A:GLY131 2.4 13.8 1.0 OD1 B:ASN119 2.5 10.1 1.0 O A:HOH312 2.5 20.7 1.0 C A:GLY131 3.3 30.8 1.0 CG B:ASN119 3.4 9.6 1.0 O A:GLY131 3.5 26.9 1.0 C B:GLN25 3.6 9.6 1.0 CG B:ASP120 3.6 9.5 1.0 ND2 B:ASN119 3.8 9.3 1.0 CB B:GLN25 4.0 8.0 1.0 CA B:ASP120 4.1 7.3 1.0 N B:ASP120 4.2 5.5 1.0 O B:HOH385 4.2 20.9 1.0 C B:ASN119 4.3 6.8 1.0 O B:HOH321 4.4 12.0 1.0 OD2 B:ASP115 4.4 19.1 1.0 CB B:ASP120 4.4 6.8 1.0 CA B:GLN25 4.4 7.8 1.0 OD2 B:ASP120 4.4 8.8 1.0 N B:SER26 4.5 9.7 1.0 O B:ASN119 4.5 6.3 1.0 CA B:SER26 4.7 10.2 1.0 OD2 B:ASP117 4.7 16.0 1.0 CA A:GLY131 4.7 23.6 1.0 CB B:ASN119 4.7 6.6 1.0 CB B:SER26 4.8 12.1 1.0 CB B:ASP117 4.9 10.7 1.0 CA B:ASN119 5.0 7.1 1.0

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