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Calcium in PDB 1b09: Human C-Reactive Protein Complexed with Phosphocholine

Protein crystallography data

The structure of Human C-Reactive Protein Complexed with Phosphocholine, PDB code: 1b09 was solved by D.Thompson, 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) 20.00 / 2.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 193.940, 193.940, 134.430, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Human C-Reactive Protein Complexed with Phosphocholine (pdb code 1b09). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Human C-Reactive Protein Complexed with Phosphocholine, PDB code: 1b09:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1b09

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Calcium binding site 1 out of 10 in the Human C-Reactive Protein Complexed with Phosphocholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human C-Reactive Protein Complexed with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:24.7
occ:1.00
 O3 A:PC500 1.7 40.4 1.0
OE1 A:GLN150 2.5 45.8 1.0
OE1 A:GLU138 2.5 56.4 1.0
OD2 A:ASP140 2.5 38.6 1.0
OD1 A:ASP140 2.8 23.8 1.0
OE2 A:GLU147 2.8 59.0 1.0
CG A:ASP140 3.0 36.2 1.0
CD A:GLN150 3.2 36.2 1.0
NE2 A:GLN150 3.2 31.7 1.0
P1 A:PC500 3.3 43.8 1.0
CD A:GLU147 3.5 52.3 1.0
CG A:GLU147 3.6 57.5 1.0
CD A:GLU138 3.7 62.0 1.0
O1 A:PC500 3.7 51.7 1.0
O4 A:PC500 3.9 40.9 1.0
O2 A:PC500 4.1 47.7 1.0
CB A:GLU147 4.2 54.4 1.0
CB A:GLU138 4.3 32.0 1.0
CA A:CA302 4.3 20.3 1.0
CG A:GLU138 4.3 46.0 1.0
CB A:ASP140 4.5 38.0 1.0
OE2 A:GLU138 4.6 55.0 1.0
OE1 A:GLU147 4.6 56.0 1.0
O A:GLU138 4.6 32.5 1.0
CG A:GLN150 4.7 25.6 1.0
O A:GLN139 4.8 46.6 1.0
C A:GLU138 4.9 23.6 1.0

Calcium binding site 2 out of 10 in 1b09

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Calcium binding site 2 out of 10 in the Human C-Reactive Protein Complexed with Phosphocholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human C-Reactive Protein Complexed with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:20.3
occ:1.00
 O1 A:PC500 1.8 51.7 1.0
OD1 A:ASN61 2.6 41.8 1.0
O A:GLN139 2.7 46.6 1.0
OD1 A:ASP140 2.7 23.8 1.0
OE2 A:GLU138 2.8 55.0 1.0
P1 A:PC500 3.0 43.8 1.0
OE1 A:GLU138 3.1 56.4 1.0
O4 A:PC500 3.1 40.9 1.0
CD A:GLU138 3.3 62.0 1.0
OD2 A:ASP60 3.3 40.4 1.0
CG A:ASN61 3.4 36.1 1.0
CG A:ASP60 3.4 35.3 1.0
O3 A:PC500 3.4 40.4 1.0
ND2 A:ASN61 3.6 39.9 1.0
OD1 A:ASP60 3.7 45.7 1.0
C A:GLN139 3.8 34.1 1.0
O A:ASP60 3.9 42.8 1.0
CG A:ASP140 3.9 36.2 1.0
CB A:ASP60 4.0 54.5 1.0
CA A:ASP140 4.1 43.2 1.0
C A:ASP60 4.2 36.9 1.0
CA A:CA301 4.3 24.7 1.0
N A:ASP140 4.4 40.7 1.0
O2 A:PC500 4.5 47.7 1.0
CB A:ASP140 4.6 38.0 1.0
N A:ASN61 4.7 20.8 1.0
CB A:ASN61 4.7 19.8 1.0
CA A:ASP60 4.8 37.9 1.0
CG A:GLU138 4.8 46.0 1.0
OD2 A:ASP140 4.8 38.6 1.0

Calcium binding site 3 out of 10 in 1b09

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Calcium binding site 3 out of 10 in the Human C-Reactive Protein Complexed with Phosphocholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human C-Reactive Protein Complexed with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:10.7
occ:1.00
 O3 B:PC500 1.6 58.1 1.0
OD1 B:ASP140 2.3 48.4 1.0
OE2 B:GLU147 2.7 54.2 1.0
OE1 B:GLU138 2.7 46.6 1.0
OE1 B:GLN150 2.8 45.9 1.0
OD2 B:ASP140 2.9 42.9 1.0
CG B:ASP140 3.0 48.3 1.0
P1 B:PC500 3.1 57.4 1.0
O1 B:PC500 3.2 52.5 1.0
NE2 B:GLN150 3.4 39.6 1.0
CD B:GLN150 3.5 41.6 1.0
CD B:GLU138 3.6 49.5 1.0
CD B:GLU147 3.8 55.5 1.0
O4 B:PC500 3.8 57.5 1.0
CA B:CA302 4.0 2.5 1.0
O2 B:PC500 4.0 42.9 1.0
CG B:GLU147 4.3 53.6 1.0
OE2 B:GLU138 4.3 35.2 1.0
CG B:GLU138 4.3 43.9 1.0
O B:GLN139 4.5 2.0 1.0
CB B:ASP140 4.5 59.7 1.0
CB B:GLU138 4.5 19.1 1.0
CB B:GLU147 4.8 57.4 1.0
OE1 B:GLU147 4.8 50.7 1.0
C B:GLN139 4.9 2.0 1.0
CG B:GLN150 5.0 16.9 1.0

Calcium binding site 4 out of 10 in 1b09

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Calcium binding site 4 out of 10 in the Human C-Reactive Protein Complexed with Phosphocholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human C-Reactive Protein Complexed with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:2.5
occ:1.00
 O1 B:PC500 1.6 52.5 1.0
O B:GLN139 2.5 2.0 1.0
ND2 B:ASN61 2.7 48.1 1.0
OE2 B:GLU138 2.8 35.2 1.0
P1 B:PC500 2.8 57.4 1.0
OD1 B:ASN61 2.9 55.5 1.0
OD2 B:ASP60 3.0 53.5 1.0
O4 B:PC500 3.0 57.5 1.0
CG B:ASN61 3.2 41.0 1.0
OD2 B:ASP140 3.2 42.9 1.0
OE1 B:GLU138 3.2 46.6 1.0
CD B:GLU138 3.4 49.5 1.0
O3 B:PC500 3.4 58.1 1.0
CG B:ASP60 3.6 59.9 1.0
CG B:ASP140 3.7 48.3 1.0
C B:GLN139 3.7 2.0 1.0
CA B:CA301 4.0 10.7 1.0
OD1 B:ASP140 4.0 48.4 1.0
CA B:ASP140 4.1 58.9 1.0
OD1 B:ASP60 4.2 52.8 1.0
O2 B:PC500 4.2 42.9 1.0
N B:ASP140 4.4 40.4 1.0
CB B:ASP60 4.5 51.8 1.0
CB B:ASP140 4.5 59.7 1.0
CB B:ASN61 4.6 42.0 1.0
CG B:GLU138 4.8 43.9 1.0
C1 B:PC500 4.9 40.6 1.0
N B:ASN61 4.9 51.0 1.0
CA B:GLN139 4.9 53.2 1.0
C B:ASP60 4.9 54.9 1.0
N B:GLN139 4.9 52.5 1.0

Calcium binding site 5 out of 10 in 1b09

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Calcium binding site 5 out of 10 in the Human C-Reactive Protein Complexed with Phosphocholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human C-Reactive Protein Complexed with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:2.0
occ:1.00
 O1 C:PC500 2.1 55.7 1.0
OE1 C:GLU147 2.3 57.2 1.0
OD2 C:ASP140 2.6 46.0 1.0
OE1 C:GLN150 2.8 45.2 1.0
OD1 C:ASP140 2.9 50.3 1.0
NE2 C:GLN150 3.0 30.9 1.0
OE1 C:GLU138 3.0 58.2 1.0
P1 C:PC500 3.1 62.9 1.0
CG C:ASP140 3.1 53.8 1.0
O3 C:PC500 3.2 31.3 1.0
CD C:GLN150 3.3 27.7 1.0
CD C:GLU147 3.4 57.5 1.0
O4 C:PC500 3.5 53.3 1.0
CD C:GLU138 3.8 52.1 1.0
CB C:GLU147 4.0 33.4 1.0
CG C:GLU147 4.0 53.5 1.0
CA C:CA302 4.2 2.0 1.0
OE2 C:GLU147 4.3 52.5 1.0
O2 C:PC500 4.5 57.8 1.0
CG C:GLU138 4.5 22.8 1.0
OE2 C:GLU138 4.5 57.5 1.0
CB C:GLU138 4.6 14.1 1.0
CB C:ASP140 4.6 40.4 1.0
CG C:GLN150 4.8 14.5 1.0
O C:GLN139 4.8 15.4 1.0

Calcium binding site 6 out of 10 in 1b09

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Calcium binding site 6 out of 10 in the Human C-Reactive Protein Complexed with Phosphocholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human C-Reactive Protein Complexed with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:2.0
occ:1.00
 O4 C:PC500 1.9 53.3 1.0
O C:GLN139 2.4 15.4 1.0
OE2 C:GLU138 2.5 57.5 1.0
OD2 C:ASP60 2.7 53.5 1.0
OD1 C:ASN61 2.9 5.5 1.0
OD1 C:ASP140 3.1 50.3 1.0
OE1 C:GLU138 3.2 58.2 1.0
CD C:GLU138 3.2 52.1 1.0
ND2 C:ASN61 3.2 33.6 1.0
O3 C:PC500 3.2 31.3 1.0
P1 C:PC500 3.2 62.9 1.0
CG C:ASN61 3.4 14.9 1.0
CG C:ASP60 3.5 48.5 1.0
C C:GLN139 3.6 19.0 1.0
CG C:ASP140 3.8 53.8 1.0
OD1 C:ASP60 4.0 54.4 1.0
CA C:ASP140 4.0 53.4 1.0
O1 C:PC500 4.2 55.7 1.0
CA C:CA301 4.2 2.0 1.0
O2 C:PC500 4.3 57.8 1.0
N C:ASP140 4.3 52.1 1.0
CB C:ASP60 4.4 40.4 1.0
OD2 C:ASP140 4.4 46.0 1.0
O C:ASP60 4.5 37.6 1.0
CB C:ASP140 4.6 40.4 1.0
CG C:GLU138 4.6 22.8 1.0
C C:ASP60 4.6 36.5 1.0
CA C:GLN139 4.8 18.4 1.0
CB C:ASN61 4.8 18.1 1.0
N C:GLN139 4.8 28.5 1.0
N C:ASN61 4.9 32.6 1.0

Calcium binding site 7 out of 10 in 1b09

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Calcium binding site 7 out of 10 in the Human C-Reactive Protein Complexed with Phosphocholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human C-Reactive Protein Complexed with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:12.7
occ:1.00
 O4 D:PC500 2.2 55.9 1.0
OE1 D:GLN150 2.4 48.7 1.0
OE2 D:GLU147 2.5 59.8 1.0
OD2 D:ASP140 2.6 22.6 1.0
OD1 D:ASP140 2.9 43.1 1.0
OE1 D:GLU138 3.0 59.8 1.0
CG D:ASP140 3.1 24.1 1.0
CD D:GLN150 3.1 16.8 1.0
NE2 D:GLN150 3.1 24.4 1.0
O1 D:PC500 3.2 52.5 1.0
P1 D:PC500 3.3 51.8 1.0
O3 D:PC500 3.3 44.2 1.0
CD D:GLU147 3.4 51.8 1.0
CG D:GLU147 3.7 56.6 1.0
CD D:GLU138 3.8 40.2 1.0
CA D:CA302 3.9 16.6 1.0
CB D:GLU147 4.2 53.6 1.0
CG D:GLU138 4.4 22.7 1.0
OE1 D:GLU147 4.5 52.6 1.0
CB D:GLU138 4.5 7.4 1.0
CB D:ASP140 4.6 17.6 1.0
CG D:GLN150 4.6 2.0 1.0
OE2 D:GLU138 4.7 38.0 1.0
O2 D:PC500 4.8 53.3 1.0
O D:GLU138 5.0 26.5 1.0

Calcium binding site 8 out of 10 in 1b09

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Calcium binding site 8 out of 10 in the Human C-Reactive Protein Complexed with Phosphocholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human C-Reactive Protein Complexed with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:16.6
occ:1.00
 O3 D:PC500 1.7 44.2 1.0
OD2 D:ASP60 2.5 36.1 1.0
OE2 D:GLU138 2.7 38.0 1.0
O D:GLN139 2.8 2.0 1.0
OE1 D:GLU138 2.9 59.8 1.0
OD1 D:ASP140 2.9 43.1 1.0
OD1 D:ASN61 3.0 49.6 1.0
CD D:GLU138 3.0 40.2 1.0
P1 D:PC500 3.2 51.8 1.0
ND2 D:ASN61 3.2 29.2 1.0
O4 D:PC500 3.4 55.9 1.0
CG D:ASN61 3.5 27.3 1.0
CG D:ASP140 3.5 24.1 1.0
CG D:ASP60 3.6 41.9 1.0
C D:GLN139 3.8 2.0 1.0
O1 D:PC500 3.9 52.5 1.0
CA D:CA301 3.9 12.7 1.0
CA D:ASP140 4.0 39.4 1.0
OD2 D:ASP140 4.0 22.6 1.0
O2 D:PC500 4.1 53.3 1.0
OD1 D:ASP60 4.1 56.9 1.0
N D:ASP140 4.2 45.2 1.0
CB D:ASP140 4.3 17.6 1.0
CG D:GLU138 4.4 22.7 1.0
O D:ASP60 4.7 32.5 1.0
CB D:ASP60 4.8 35.5 1.0
CB D:ASN61 4.9 9.9 1.0
C D:ASP60 5.0 22.3 1.0

Calcium binding site 9 out of 10 in 1b09

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Calcium binding site 9 out of 10 in the Human C-Reactive Protein Complexed with Phosphocholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Human C-Reactive Protein Complexed with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca301

b:22.7
occ:1.00
 O3 E:PC500 1.8 41.3 1.0
OE1 E:GLN150 2.3 44.1 1.0
OD2 E:ASP140 2.4 30.0 1.0
OD1 E:ASP140 2.6 35.7 1.0
OE1 E:GLU138 2.7 41.3 1.0
CG E:ASP140 2.8 18.4 1.0
OE1 E:GLU147 2.9 58.9 1.0
CD E:GLN150 3.3 19.6 1.0
P1 E:PC500 3.3 35.5 1.0
CA E:CA302 3.4 18.5 1.0
O4 E:PC500 3.5 56.2 1.0
NE2 E:GLN150 3.6 11.3 1.0
CD E:GLU138 3.7 20.2 1.0
O1 E:PC500 3.8 57.6 1.0
CD E:GLU147 4.0 58.0 1.0
CB E:GLU147 4.1 53.5 1.0
O2 E:PC500 4.2 45.1 1.0
CB E:ASP140 4.4 12.3 1.0
CG E:GLU138 4.4 13.8 1.0
O E:GLU138 4.4 33.4 1.0
OE2 E:GLU138 4.5 17.8 1.0
CB E:GLU138 4.5 16.9 1.0
CG E:GLU147 4.6 52.4 1.0
CG E:GLN150 4.7 2.0 1.0
O E:GLN139 4.8 2.0 1.0
OE2 E:GLU147 4.9 50.0 1.0
C E:GLU138 5.0 20.7 1.0

Calcium binding site 10 out of 10 in 1b09

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Calcium binding site 10 out of 10 in the Human C-Reactive Protein Complexed with Phosphocholine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Human C-Reactive Protein Complexed with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:18.5
occ:1.00
 O1 E:PC500 1.8 57.6 1.0
OD1 E:ASP140 2.4 35.7 1.0
OE1 E:GLU138 2.5 41.3 1.0
OE2 E:GLU138 2.6 17.8 1.0
O E:GLN139 2.7 2.0 1.0
O3 E:PC500 2.7 41.3 1.0
OD2 E:ASP60 2.8 16.3 1.0
CD E:GLU138 2.9 20.2 1.0
P1 E:PC500 3.0 35.5 1.0
OD1 E:ASN61 3.2 21.1 1.0
ND2 E:ASN61 3.3 20.5 1.0
CA E:CA301 3.4 22.7 1.0
CG E:ASP140 3.5 18.4 1.0
CG E:ASN61 3.6 17.8 1.0
C E:GLN139 3.7 2.0 1.0
O4 E:PC500 3.8 56.2 1.0
CA E:ASP140 3.9 47.1 1.0
CG E:ASP60 4.0 18.6 1.0
N E:ASP140 4.2 53.1 1.0
OD2 E:ASP140 4.2 30.0 1.0
O2 E:PC500 4.2 45.1 1.0
CB E:ASP140 4.3 12.3 1.0
CG E:GLU138 4.4 13.8 1.0
OD1 E:ASP60 4.7 13.6 1.0
C1 E:PC500 4.8 33.5 1.0
CA E:GLN139 4.9 2.0 1.0
N E:GLN139 4.9 2.0 1.0
O E:ASP60 4.9 23.2 1.0

Reference:

D.Thompson, M.B.Pepys, S.P.Wood. The Physiological Structure of Human C-Reactive Protein and Its Complex with Phosphocholine. Structure Fold.Des. V. 7 169 1999.
ISSN: ISSN 0969-2126
PubMed: 10368284
DOI: 10.1016/S0969-2126(99)80023-9
Page generated: Thu Jul 11 06:12:28 2024

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