Calcium in PDB 1gyk: Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH

The structure of Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH, PDB code: 1gyk was solved by D.Thompson, M.B.Pepys, I.Tickle, S.P.Wood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20 / 2.2
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.760, 70.530, 103.410, 90.00, 96.80, 90.00
R / Rfree (%)	18.6 / 22.4

The binding sites of Calcium atom in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH (pdb code 1gyk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH, PDB code: 1gyk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1205 b:14.2 occ:1.00 OD1 A:ASN59 2.2 15.4 1.0 OD1 A:ASP58 2.3 15.7 1.0 O A:GLN137 2.4 13.9 1.0 OD1 A:ASP138 2.5 20.7 1.0 O8B A:CDG1207 2.5 20.9 1.0 OE2 A:GLU136 2.6 13.7 1.0 OE1 A:GLU136 2.6 13.1 1.0 OD2 A:ASP58 2.9 16.8 1.0 CD A:GLU136 2.9 15.5 1.0 CG A:ASP58 2.9 14.8 1.0 CG A:ASN59 3.3 13.7 1.0 C A:GLN137 3.5 15.3 1.0 C8 A:CDG1207 3.6 24.0 1.0 CG A:ASP138 3.6 18.3 1.0 ND2 A:ASN59 3.8 8.5 1.0 CA A:ASP138 3.9 19.6 1.0 O8A A:CDG1207 4.0 14.4 1.0 CA A:CA1206 4.1 15.0 1.0 N A:ASP138 4.1 15.8 1.0 N A:ASN59 4.3 14.8 1.0 CB A:ASP138 4.3 17.9 1.0 CG A:GLU136 4.4 13.1 1.0 CB A:ASP58 4.4 14.1 1.0 OD2 A:ASP138 4.6 16.7 1.0 CB A:ASN59 4.6 11.1 1.0 ND2 A:ASN53 4.6 11.2 1.0 N A:GLN137 4.6 11.1 1.0 CA A:GLN137 4.6 13.6 1.0 OD1 A:ASN53 4.7 17.3 1.0 CA A:ASN59 4.8 14.1 1.0 C7 A:CDG1207 4.9 25.1 1.0 C A:ASP58 4.9 13.1 1.0

Calcium binding site 2 out of 9 in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1206 b:15.0 occ:1.00 OE1 A:GLN148 2.2 15.6 1.0 OE1 A:GLU136 2.3 13.1 1.0 O8A A:CDG1207 2.4 14.4 1.0 OD2 A:ASP138 2.4 16.7 1.0 OD1 A:ASP138 2.7 20.7 1.0 CG A:ASP138 2.8 18.3 1.0 CD A:GLN148 3.2 14.4 1.0 C8 A:CDG1207 3.4 24.0 1.0 CD A:GLU136 3.4 15.5 1.0 NE2 A:GLN148 3.6 15.2 1.0 O8B A:CDG1207 3.7 20.9 1.0 CG A:GLU136 4.0 13.1 1.0 CA A:CA1205 4.1 14.2 1.0 CB A:GLU136 4.2 13.4 1.0 CB A:ASP138 4.2 17.9 1.0 CB A:ASP145 4.3 21.1 1.0 OE2 A:GLU136 4.4 13.7 1.0 O A:GLU136 4.5 11.2 1.0 CG A:GLN148 4.5 11.0 1.0 O A:GLN137 4.6 13.9 1.0 OD2 A:ASP145 4.7 26.1 1.0 C7 A:CDG1207 4.7 25.1 1.0 O A:LYS143 4.8 25.7 1.0 C A:GLU136 4.9 9.3 1.0 O4 A:CDG1207 4.9 34.0 1.0 C A:GLN137 4.9 15.3 1.0 N A:ASP138 5.0 15.8 1.0 CA A:ASP138 5.0 19.6 1.0

Calcium binding site 3 out of 9 in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1205 b:14.2 occ:1.00 OD1 B:ASN59 2.2 15.4 1.0 OD1 B:ASP58 2.3 15.7 1.0 O B:GLN137 2.4 13.9 1.0 OD1 B:ASP138 2.5 20.7 1.0 O8B B:CDG1207 2.5 20.9 1.0 OE2 B:GLU136 2.6 13.7 1.0 OE1 B:GLU136 2.6 13.1 1.0 OD2 B:ASP58 2.9 16.8 1.0 CD B:GLU136 2.9 15.5 1.0 CG B:ASP58 2.9 14.8 1.0 CG B:ASN59 3.3 13.7 1.0 C B:GLN137 3.5 15.3 1.0 C8 B:CDG1207 3.6 24.0 1.0 CG B:ASP138 3.6 18.3 1.0 ND2 B:ASN59 3.8 8.5 1.0 CA B:ASP138 3.9 19.6 1.0 O8A B:CDG1207 4.0 14.4 1.0 CA B:CA1206 4.1 15.0 1.0 N B:ASP138 4.1 15.8 1.0 N B:ASN59 4.3 14.8 1.0 CB B:ASP138 4.3 17.9 1.0 CG B:GLU136 4.4 13.1 1.0 CB B:ASP58 4.4 14.1 1.0 OD2 B:ASP138 4.6 16.7 1.0 CB B:ASN59 4.6 11.1 1.0 ND2 B:ASN53 4.6 11.2 1.0 N B:GLN137 4.6 11.1 1.0 CA B:GLN137 4.6 13.6 1.0 OD1 B:ASN53 4.7 17.3 1.0 CA B:ASN59 4.8 14.1 1.0 C7 B:CDG1207 4.9 25.1 1.0 C B:ASP58 4.9 13.1 1.0

Calcium binding site 4 out of 9 in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1206 b:15.0 occ:1.00 OE1 B:GLN148 2.2 15.6 1.0 OE1 B:GLU136 2.3 13.1 1.0 O8A B:CDG1207 2.4 14.4 1.0 OD2 B:ASP138 2.4 16.7 1.0 OD1 B:ASP138 2.7 20.7 1.0 CG B:ASP138 2.8 18.3 1.0 CD B:GLN148 3.2 14.4 1.0 C8 B:CDG1207 3.4 24.0 1.0 CD B:GLU136 3.4 15.5 1.0 NE2 B:GLN148 3.6 15.2 1.0 O8B B:CDG1207 3.7 20.9 1.0 CG B:GLU136 4.0 13.1 1.0 CA B:CA1205 4.1 14.2 1.0 CB B:GLU136 4.2 13.4 1.0 CB B:ASP138 4.2 17.9 1.0 CB B:ASP145 4.3 21.1 1.0 OE2 B:GLU136 4.4 13.7 1.0 O B:GLU136 4.5 11.2 1.0 CG B:GLN148 4.5 11.0 1.0 O B:GLN137 4.6 13.9 1.0 OD2 B:ASP145 4.7 26.1 1.0 C7 B:CDG1207 4.7 25.1 1.0 O B:LYS143 4.8 25.7 1.0 C B:GLU136 4.9 9.3 1.0 O4 B:CDG1207 4.9 34.0 1.0 C B:GLN137 4.9 15.3 1.0 N B:ASP138 5.0 15.8 1.0 CA B:ASP138 5.0 19.6 1.0

Calcium binding site 5 out of 9 in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1205 b:14.2 occ:1.00 OD1 C:ASN59 2.2 15.4 1.0 OD1 C:ASP58 2.3 15.7 1.0 O C:GLN137 2.4 13.9 1.0 OD1 C:ASP138 2.5 20.7 1.0 O8B C:CDG1207 2.5 20.9 1.0 OE2 C:GLU136 2.6 13.7 1.0 OE1 C:GLU136 2.6 13.1 1.0 OD2 C:ASP58 2.9 16.8 1.0 CD C:GLU136 2.9 15.5 1.0 CG C:ASP58 2.9 14.8 1.0 CG C:ASN59 3.3 13.7 1.0 C C:GLN137 3.5 15.3 1.0 C8 C:CDG1207 3.6 24.0 1.0 CG C:ASP138 3.6 18.3 1.0 ND2 C:ASN59 3.8 8.5 1.0 CA C:ASP138 3.9 19.6 1.0 O8A C:CDG1207 4.0 14.4 1.0 CA C:CA1206 4.1 15.0 1.0 N C:ASP138 4.1 15.8 1.0 N C:ASN59 4.3 14.8 1.0 CB C:ASP138 4.3 17.9 1.0 CG C:GLU136 4.4 13.1 1.0 CB C:ASP58 4.4 14.1 1.0 OD2 C:ASP138 4.6 16.7 1.0 CB C:ASN59 4.6 11.1 1.0 ND2 C:ASN53 4.6 11.2 1.0 N C:GLN137 4.6 11.1 1.0 CA C:GLN137 4.6 13.6 1.0 OD1 C:ASN53 4.7 17.3 1.0 CA C:ASN59 4.8 14.1 1.0 C7 C:CDG1207 4.9 25.1 1.0 C C:ASP58 4.9 13.1 1.0

Calcium binding site 6 out of 9 in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1206 b:15.0 occ:1.00 OE1 C:GLN148 2.2 15.6 1.0 OE1 C:GLU136 2.3 13.1 1.0 O8A C:CDG1207 2.4 14.4 1.0 OD2 C:ASP138 2.4 16.7 1.0 OD1 C:ASP138 2.7 20.7 1.0 CG C:ASP138 2.8 18.3 1.0 CD C:GLN148 3.2 14.4 1.0 C8 C:CDG1207 3.4 24.0 1.0 CD C:GLU136 3.4 15.5 1.0 NE2 C:GLN148 3.6 15.2 1.0 O8B C:CDG1207 3.7 20.9 1.0 CG C:GLU136 4.0 13.1 1.0 CA C:CA1205 4.1 14.2 1.0 CB C:GLU136 4.2 13.4 1.0 CB C:ASP145 4.2 21.1 1.0 CB C:ASP138 4.2 17.9 1.0 OE2 C:GLU136 4.4 13.7 1.0 O C:GLU136 4.5 11.2 1.0 CG C:GLN148 4.5 11.0 1.0 O C:GLN137 4.6 13.9 1.0 C7 C:CDG1207 4.7 25.1 1.0 OD2 C:ASP145 4.7 26.1 1.0 O C:LYS143 4.8 25.7 1.0 C C:GLU136 4.9 9.3 1.0 O4 C:CDG1207 4.9 34.0 1.0 C C:GLN137 4.9 15.3 1.0 N C:ASP138 5.0 15.8 1.0 CA C:ASP138 5.0 19.6 1.0

Calcium binding site 7 out of 9 in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1205 b:14.2 occ:1.00 OD1 D:ASN59 2.2 15.4 1.0 OD1 D:ASP58 2.3 15.7 1.0 O D:GLN137 2.4 13.9 1.0 OD1 D:ASP138 2.5 20.7 1.0 O8B D:CDG1207 2.5 20.9 1.0 OE2 D:GLU136 2.6 13.7 1.0 OE1 D:GLU136 2.6 13.1 1.0 OD2 D:ASP58 2.9 16.8 1.0 CD D:GLU136 2.9 15.5 1.0 CG D:ASP58 2.9 14.8 1.0 CG D:ASN59 3.3 13.7 1.0 C D:GLN137 3.5 15.3 1.0 C8 D:CDG1207 3.6 24.0 1.0 CG D:ASP138 3.6 18.3 1.0 ND2 D:ASN59 3.8 8.5 1.0 CA D:ASP138 3.9 19.6 1.0 O8A D:CDG1207 4.0 14.4 1.0 CA D:CA1206 4.1 15.0 1.0 N D:ASP138 4.1 15.8 1.0 N D:ASN59 4.3 14.8 1.0 CB D:ASP138 4.3 17.9 1.0 CG D:GLU136 4.4 13.1 1.0 CB D:ASP58 4.4 14.1 1.0 OD2 D:ASP138 4.6 16.7 1.0 CB D:ASN59 4.6 11.1 1.0 ND2 D:ASN53 4.6 11.2 1.0 N D:GLN137 4.6 11.1 1.0 CA D:GLN137 4.6 13.6 1.0 OD1 D:ASN53 4.7 17.3 1.0 CA D:ASN59 4.8 14.1 1.0 C7 D:CDG1207 4.9 25.1 1.0 C D:ASP58 4.9 13.1 1.0

Calcium binding site 8 out of 9 in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1206 b:15.0 occ:1.00 OE1 D:GLN148 2.2 15.6 1.0 OE1 D:GLU136 2.3 13.1 1.0 O8A D:CDG1207 2.4 14.4 1.0 OD2 D:ASP138 2.4 16.7 1.0 OD1 D:ASP138 2.7 20.7 1.0 CG D:ASP138 2.8 18.3 1.0 CD D:GLN148 3.2 14.4 1.0 C8 D:CDG1207 3.4 24.0 1.0 CD D:GLU136 3.4 15.5 1.0 NE2 D:GLN148 3.6 15.2 1.0 O8B D:CDG1207 3.7 20.9 1.0 CG D:GLU136 4.0 13.1 1.0 CA D:CA1205 4.1 14.2 1.0 CB D:GLU136 4.2 13.4 1.0 CB D:ASP138 4.2 17.9 1.0 CB D:ASP145 4.3 21.1 1.0 OE2 D:GLU136 4.4 13.7 1.0 O D:GLU136 4.5 11.2 1.0 CG D:GLN148 4.5 11.0 1.0 O D:GLN137 4.6 13.9 1.0 OD2 D:ASP145 4.7 26.1 1.0 C7 D:CDG1207 4.7 25.1 1.0 O D:LYS143 4.8 25.7 1.0 C D:GLU136 4.9 9.3 1.0 O4 D:CDG1207 4.9 34.0 1.0 C D:GLN137 4.9 15.3 1.0 N D:ASP138 5.0 15.8 1.0 CA D:ASP138 5.0 19.6 1.0

Calcium binding site 9 out of 9 in the Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Serum Amyloid P Component Co-Crystallised with Mobdg at Neutral pH within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca1205 b:33.1 occ:1.00 O E:GLN137 2.2 24.6 1.0 OD1 E:ASP58 2.4 25.8 1.0 OD1 E:ASN59 2.6 26.6 1.0 OD1 E:ASP138 2.6 27.8 1.0 OE1 E:GLU136 2.6 28.9 1.0 OE2 E:GLU136 2.6 23.4 1.0 OD2 E:ASP58 2.9 25.3 1.0 CD E:GLU136 3.0 21.7 1.0 CG E:ASP58 3.0 29.8 1.0 C E:GLN137 3.4 25.5 1.0 CG E:ASN59 3.4 23.9 1.0 CG E:ASP138 3.7 32.5 1.0 ND2 E:ASN59 3.8 23.5 1.0 CA E:ASP138 3.9 32.8 1.0 N E:ASP138 4.0 28.2 1.0 CB E:ASP138 4.4 31.6 1.0 CG E:GLU136 4.4 23.2 1.0 N E:ASN59 4.5 30.1 1.0 CB E:ASP58 4.5 31.9 1.0 N E:GLN137 4.5 23.0 1.0 CA E:GLN137 4.6 22.5 1.0 ND2 E:ASN53 4.7 24.8 1.0 CB E:ASN59 4.7 26.7 1.0 OD2 E:ASP138 4.8 34.1 1.0 CA E:ASN59 5.0 26.8 1.0

D.Thompson, M.B.Pepys, I.Tickle, S.P.Wood. The Structures of Crystalline Complexes of Human Serum Amyloid P Component with Its Carbohydrate Ligand, the Cyclic Pyruvate Acetal of Galactose J.Mol.Biol. V. 320 1081 2002.
ISSN: ISSN 0022-2836
PubMed: 12126626
DOI: 10.1016/S0022-2836(02)00514-4