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Calcium in PDB 1sac: The Structure of Pentameric Human Serum Amyloid P Component

Protein crystallography data

The structure of The Structure of Pentameric Human Serum Amyloid P Component, PDB code: 1sac was solved by H.E.White, J.Emsley, B.P.O'hara, G.Oliva, N.Srinivasan, I.J.Tickle, T.L.Blundell, M.B.Pepys, S.P.Wood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.900, 99.300, 96.700, 90.00, 95.90, 90.00
R / Rfree (%) n/a / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of Pentameric Human Serum Amyloid P Component (pdb code 1sac). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the The Structure of Pentameric Human Serum Amyloid P Component, PDB code: 1sac:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1sac

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Calcium binding site 1 out of 10 in the The Structure of Pentameric Human Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of Pentameric Human Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:14.2
occ:1.00
 O A:GLN137 2.5 20.0 1.0
OD1 A:ASN59 2.5 18.1 1.0
OD1 A:ASP138 2.5 18.5 1.0
OE2 A:GLU136 2.6 17.2 1.0
OD1 A:ASP58 2.7 21.4 1.0
O A:ACY300 2.7 25.0 1.0
OD2 A:ASP58 2.8 23.0 1.0
OE1 A:GLU136 2.8 17.0 1.0
CG A:ASP58 3.0 20.4 1.0
CD A:GLU136 3.1 16.4 1.0
C A:ACY300 3.3 24.6 1.0
CG A:ASN59 3.4 16.8 1.0
ND2 A:ASN59 3.6 18.2 1.0
C A:GLN137 3.6 18.2 1.0
CG A:ASP138 3.8 18.1 1.0
CA A:ASP138 3.9 19.1 1.0
OXT A:ACY300 4.0 23.8 1.0
CA A:CA206 4.0 21.4 1.0
N A:ASP138 4.2 19.2 1.0
CH3 A:ACY300 4.2 25.3 1.0
N A:ASN59 4.5 16.5 1.0
CB A:ASP138 4.5 18.3 1.0
CB A:ASP58 4.6 19.5 1.0
CG A:GLU136 4.6 16.0 1.0
CB A:ASN59 4.7 16.6 1.0
OD2 A:ASP138 4.7 21.8 1.0
CA A:GLN137 4.8 16.8 1.0
N A:GLN137 4.8 15.7 1.0
ND2 A:ASN53 4.9 12.4 1.0
CA A:ASN59 4.9 15.7 1.0
OD1 A:ASN53 5.0 15.0 1.0

Calcium binding site 2 out of 10 in 1sac

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Calcium binding site 2 out of 10 in the The Structure of Pentameric Human Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of Pentameric Human Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:21.4
occ:1.00
 OE1 A:GLU136 2.4 17.0 1.0
OE1 A:GLN148 2.6 19.6 1.0
OXT A:ACY300 2.7 23.8 1.0
OD2 A:ASP138 2.7 21.8 1.0
OD1 A:ASP138 2.8 18.5 1.0
CG A:ASP138 3.0 18.1 1.0
C A:ACY300 3.5 24.6 1.0
CD A:GLN148 3.5 17.5 1.0
CD A:GLU136 3.7 16.4 1.0
O A:ACY300 3.8 25.0 1.0
NE2 A:GLN148 3.9 19.5 1.0
CA A:CA205 4.0 14.2 1.0
CB A:ASP145 4.2 24.2 1.0
CB A:ASP138 4.4 18.3 1.0
CB A:GLU136 4.4 15.3 1.0
O A:GLU136 4.4 14.8 1.0
CG A:GLU136 4.5 16.0 1.0
OE2 A:GLU136 4.6 17.2 1.0
O A:GLN137 4.6 20.0 1.0
O A:LYS143 4.7 21.9 1.0
CG A:GLN148 4.7 17.8 1.0
OD2 A:ASP145 4.8 28.4 1.0
CH3 A:ACY300 4.8 25.3 1.0
C A:GLU136 4.8 15.9 1.0
C A:GLN137 4.8 18.2 1.0
N A:ASP138 4.9 19.2 1.0
CA A:ASP138 4.9 19.1 1.0

Calcium binding site 3 out of 10 in 1sac

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Calcium binding site 3 out of 10 in the The Structure of Pentameric Human Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of Pentameric Human Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca205

b:22.8
occ:1.00
 O B:GLN137 2.5 14.5 1.0
OD1 B:ASN59 2.5 16.2 1.0
OD1 B:ASP138 2.5 17.0 1.0
OD1 B:ASP58 2.6 22.7 1.0
OE2 B:GLU136 2.6 16.0 1.0
O B:ACY300 2.7 22.4 1.0
OD2 B:ASP58 2.8 22.4 1.0
OE1 B:GLU136 2.8 15.3 1.0
CG B:ASP58 3.0 23.6 1.0
CD B:GLU136 3.1 14.4 1.0
C B:ACY300 3.3 20.8 1.0
CG B:ASN59 3.5 17.1 1.0
OXT B:ACY300 3.6 19.4 1.0
C B:GLN137 3.7 14.6 1.0
CG B:ASP138 3.8 16.7 1.0
ND2 B:ASN59 3.8 17.1 1.0
CA B:ASP138 3.9 16.2 1.0
CA B:CA206 4.0 24.5 1.0
N B:ASP138 4.3 16.1 1.0
CB B:ASP138 4.5 15.8 1.0
N B:ASN59 4.5 20.5 1.0
CH3 B:ACY300 4.5 20.9 1.0
CB B:ASP58 4.6 21.6 1.0
CG B:GLU136 4.7 12.2 1.0
CB B:ASN59 4.7 17.8 1.0
OD2 B:ASP138 4.8 18.4 1.0
ND2 B:ASN53 4.8 14.5 1.0
N B:GLN137 4.8 12.3 1.0
CA B:GLN137 4.8 13.6 1.0
CD2 B:LEU62 4.8 8.0 1.0
OD1 B:ASN53 4.9 15.2 1.0
CA B:ASN59 4.9 18.2 1.0

Calcium binding site 4 out of 10 in 1sac

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Calcium binding site 4 out of 10 in the The Structure of Pentameric Human Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of Pentameric Human Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca206

b:24.5
occ:1.00
 OE1 B:GLU136 2.4 15.3 1.0
OE1 B:GLN148 2.6 16.5 1.0
OD1 B:ASP138 2.6 17.0 1.0
OXT B:ACY300 2.7 19.4 1.0
OD2 B:ASP138 2.8 18.4 1.0
CG B:ASP138 3.0 16.7 1.0
CD B:GLU136 3.6 14.4 1.0
CD B:GLN148 3.7 16.1 1.0
C B:ACY300 3.7 20.8 1.0
CA B:CA205 4.0 22.8 1.0
O B:GLU136 4.0 13.8 1.0
CB B:ASP145 4.1 19.2 1.0
NE2 B:GLN148 4.1 16.4 1.0
CB B:GLU136 4.1 12.0 1.0
O B:ACY300 4.3 22.4 1.0
CB B:ASP138 4.3 15.8 1.0
CG B:GLU136 4.3 12.2 1.0
OE2 B:GLU136 4.4 16.0 1.0
O B:GLN137 4.5 14.5 1.0
O B:LYS143 4.5 21.2 1.0
OD2 B:ASP145 4.5 20.7 1.0
C B:GLU136 4.6 13.1 1.0
C B:GLN137 4.6 14.6 1.0
CH3 B:ACY300 4.8 20.9 1.0
CG B:ASP145 4.8 20.8 1.0
N B:ASP138 4.8 16.1 1.0
CA B:ASP138 4.9 16.2 1.0
CG B:GLN148 5.0 15.5 1.0

Calcium binding site 5 out of 10 in 1sac

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Calcium binding site 5 out of 10 in the The Structure of Pentameric Human Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structure of Pentameric Human Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca205

b:18.8
occ:1.00
 O C:GLN137 2.5 13.7 1.0
OE2 C:GLU136 2.5 15.7 1.0
OD1 C:ASP138 2.5 19.0 1.0
OD1 C:ASN59 2.6 18.2 1.0
OD2 C:ASP58 2.7 17.0 1.0
OD1 C:ASP58 2.7 18.4 1.0
OE1 C:GLU136 2.8 15.3 1.0
CG C:ASP58 3.0 17.5 1.0
CD C:GLU136 3.0 13.2 1.0
CG C:ASN59 3.5 16.5 1.0
C C:GLN137 3.7 13.4 1.0
ND2 C:ASN59 3.7 15.5 1.0
CG C:ASP138 3.8 18.2 1.0
CA C:CA206 3.9 20.4 1.0
CA C:ASP138 4.0 15.7 1.0
N C:ASP138 4.3 13.7 1.0
CB C:ASP58 4.5 18.0 1.0
N C:ASN59 4.5 16.0 1.0
CB C:ASP138 4.5 15.7 1.0
CG C:GLU136 4.5 12.8 1.0
CB C:ASN59 4.7 17.0 1.0
OD2 C:ASP138 4.7 19.4 1.0
CA C:GLN137 4.9 12.7 1.0
N C:GLN137 4.9 12.1 1.0
CD2 C:LEU62 4.9 9.5 1.0
OD1 C:ASN53 4.9 12.1 1.0
ND2 C:ASN53 4.9 15.1 1.0
CA C:ASN59 5.0 16.0 1.0

Calcium binding site 6 out of 10 in 1sac

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Calcium binding site 6 out of 10 in the The Structure of Pentameric Human Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structure of Pentameric Human Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca206

b:20.4
occ:1.00
 OE1 C:GLN148 2.5 15.2 1.0
OE1 C:GLU136 2.5 15.3 1.0
OD1 C:ASP138 2.6 19.0 1.0
OD2 C:ASP138 2.7 19.4 1.0
CG C:ASP138 2.9 18.2 1.0
CD C:GLN148 3.5 16.1 1.0
CD C:GLU136 3.7 13.2 1.0
NE2 C:GLN148 3.9 17.4 1.0
CA C:CA205 3.9 18.8 1.0
CB C:ASP145 4.1 20.9 1.0
CB C:ASP138 4.2 15.7 1.0
O C:GLU136 4.3 14.6 1.0
OD2 C:ASP145 4.4 22.5 1.0
O C:GLN137 4.6 13.7 1.0
CG C:GLU136 4.6 12.8 1.0
OE2 C:GLU136 4.6 15.7 1.0
CB C:GLU136 4.6 13.1 1.0
O C:LYS143 4.7 22.7 1.0
CG C:ASP145 4.8 21.7 1.0
CG C:GLN148 4.8 16.6 1.0
CA C:ASP138 4.9 15.7 1.0
C C:GLN137 4.9 13.4 1.0
C C:GLU136 4.9 11.6 1.0

Calcium binding site 7 out of 10 in 1sac

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Calcium binding site 7 out of 10 in the The Structure of Pentameric Human Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structure of Pentameric Human Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca205

b:27.6
occ:1.00
 OD1 D:ASP138 2.3 23.4 1.0
O D:GLN137 2.4 18.9 1.0
OD1 D:ASP58 2.5 24.4 1.0
OE2 D:GLU136 2.6 19.3 1.0
OE1 D:GLU136 2.7 19.3 1.0
O D:ACY300 2.7 33.2 1.0
OD1 D:ASN59 2.7 21.1 1.0
OD2 D:ASP58 2.8 23.1 1.0
CG D:ASP58 3.0 24.0 1.0
CD D:GLU136 3.0 17.9 1.0
CG D:ASN59 3.4 21.0 1.0
ND2 D:ASN59 3.5 22.3 1.0
C D:ACY300 3.5 34.6 1.0
C D:GLN137 3.5 20.0 1.0
CG D:ASP138 3.6 24.7 1.0
OXT D:ACY300 3.8 34.9 1.0
CA D:ASP138 3.9 22.8 1.0
CA D:CA206 4.1 27.8 1.0
N D:ASP138 4.2 20.9 1.0
CB D:ASP138 4.4 24.4 1.0
N D:ASN59 4.4 23.6 1.0
CB D:ASP58 4.5 24.3 1.0
OD2 D:ASP138 4.5 27.0 1.0
CG D:GLU136 4.5 16.9 1.0
ND2 D:ASN53 4.6 19.8 1.0
CH3 D:ACY300 4.7 35.1 1.0
CB D:ASN59 4.7 20.8 1.0
CA D:GLN137 4.8 19.1 1.0
N D:GLN137 4.8 18.2 1.0
CA D:ASN59 4.9 22.9 1.0
CD2 D:LEU62 4.9 13.1 1.0

Calcium binding site 8 out of 10 in 1sac

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Calcium binding site 8 out of 10 in the The Structure of Pentameric Human Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structure of Pentameric Human Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca206

b:27.8
occ:1.00
 OE1 D:GLN148 2.5 19.6 1.0
OE1 D:GLU136 2.6 19.3 1.0
OD2 D:ASP138 2.6 27.0 1.0
OXT D:ACY300 2.7 34.9 1.0
OD1 D:ASP138 2.9 23.4 1.0
CG D:ASP138 2.9 24.7 1.0
CD D:GLN148 3.6 18.6 1.0
C D:ACY300 3.7 34.6 1.0
CD D:GLU136 3.8 17.9 1.0
O D:ACY300 4.0 33.2 1.0
NE2 D:GLN148 4.0 22.3 1.0
CA D:CA205 4.1 27.6 1.0
CB D:ASP145 4.1 22.9 1.0
CB D:ASP138 4.2 24.4 1.0
O D:GLU136 4.3 18.1 1.0
O D:GLN137 4.4 18.9 1.0
CB D:GLU136 4.5 16.3 1.0
OD2 D:ASP145 4.5 22.8 1.0
CG D:GLU136 4.5 16.9 1.0
O D:LYS143 4.6 25.5 1.0
OE2 D:GLU136 4.7 19.3 1.0
C D:GLN137 4.8 20.0 1.0
C D:GLU136 4.8 17.7 1.0
CG D:ASP145 4.9 23.1 1.0
CG D:GLN148 4.9 18.3 1.0
CA D:ASP138 5.0 22.8 1.0

Calcium binding site 9 out of 10 in 1sac

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Calcium binding site 9 out of 10 in the The Structure of Pentameric Human Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of The Structure of Pentameric Human Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca205

b:20.6
occ:1.00
 O E:GLN137 2.4 18.2 1.0
OD1 E:ASP58 2.5 21.6 1.0
OD1 E:ASP138 2.5 20.0 1.0
OE2 E:GLU136 2.5 17.8 1.0
O E:ACY300 2.6 18.8 1.0
OD1 E:ASN59 2.6 14.2 1.0
OE1 E:GLU136 2.9 18.2 1.0
OD2 E:ASP58 2.9 18.9 1.0
CG E:ASP58 3.1 19.6 1.0
CD E:GLU136 3.1 17.9 1.0
CG E:ASN59 3.5 13.8 1.0
C E:GLN137 3.6 18.6 1.0
C E:ACY300 3.6 19.7 1.0
CG E:ASP138 3.8 22.9 1.0
ND2 E:ASN59 3.8 12.9 1.0
CA E:ASP138 3.9 21.7 1.0
OXT E:ACY300 4.0 23.5 1.0
CA E:CA206 4.1 25.2 1.0
N E:ASP138 4.2 20.8 1.0
CB E:ASP138 4.4 22.0 1.0
N E:ASN59 4.5 16.5 1.0
CB E:ASP58 4.6 18.4 1.0
CG E:GLU136 4.6 15.5 1.0
CH3 E:ACY300 4.7 20.4 1.0
OD2 E:ASP138 4.7 23.5 1.0
CB E:ASN59 4.8 13.6 1.0
ND2 E:ASN53 4.8 18.4 1.0
CA E:GLN137 4.8 19.1 1.0
N E:GLN137 4.9 17.8 1.0
CA E:ASN59 5.0 15.3 1.0

Calcium binding site 10 out of 10 in 1sac

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Calcium binding site 10 out of 10 in the The Structure of Pentameric Human Serum Amyloid P Component


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of The Structure of Pentameric Human Serum Amyloid P Component within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca206

b:25.2
occ:1.00
 OE1 E:GLU136 2.4 18.2 1.0
OE1 E:GLN148 2.6 18.1 1.0
OXT E:ACY300 2.7 23.5 1.0
OD2 E:ASP138 2.7 23.5 1.0
OD1 E:ASP138 2.8 20.0 1.0
CG E:ASP138 2.9 22.9 1.0
CD E:GLN148 3.6 17.5 1.0
C E:ACY300 3.7 19.7 1.0
CD E:GLU136 3.7 17.9 1.0
O E:ACY300 3.8 18.8 1.0
NE2 E:GLN148 3.9 17.1 1.0
CB E:ASP145 4.0 20.2 1.0
CA E:CA205 4.1 20.6 1.0
CB E:ASP138 4.2 22.0 1.0
O E:GLU136 4.2 18.1 1.0
OD2 E:ASP145 4.4 24.0 1.0
CB E:GLU136 4.5 14.2 1.0
O E:GLN137 4.6 18.2 1.0
CG E:GLU136 4.6 15.5 1.0
OE2 E:GLU136 4.6 17.8 1.0
O E:LYS143 4.7 23.4 1.0
CG E:ASP145 4.7 22.0 1.0
C E:GLU136 4.8 17.5 1.0
CA E:ASP138 4.9 21.7 1.0
C E:GLN137 4.9 18.6 1.0
CG E:GLN148 4.9 15.4 1.0

Reference:

J.Emsley, H.E.White, B.P.O'hara, G.Oliva, N.Srinivasan, I.J.Tickle, T.L.Blundell, M.B.Pepys, S.P.Wood. Structure of Pentameric Human Serum Amyloid P Component. Nature V. 367 338 1994.
ISSN: ISSN 0028-0836
PubMed: 8114934
DOI: 10.1038/367338A0
Page generated: Sat Dec 12 03:18:56 2020

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