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

Protein crystallography data

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

Calcium Binding Sites:

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 1gyk

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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 1gyk

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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 1gyk

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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 1gyk

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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 1gyk

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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 1gyk

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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 1gyk

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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 1gyk

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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 1gyk

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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

Reference:

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
Page generated: Mon Jul 7 15:26:13 2025

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