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Calcium in PDB 3pvo: Monoclinic Form of Human C-Reactive Protein

Protein crystallography data

The structure of Monoclinic Form of Human C-Reactive Protein, PDB code: 3pvo was solved by C.Guillon, U.Mavoungou Bigouagou, P.Jeannin, Y.Delneste, P.Gouet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 97.600, 143.200, 161.200, 90.00, 89.70, 90.00
R / Rfree (%) 22.7 / 28.5

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Calcium atom in the Monoclinic Form of Human C-Reactive Protein (pdb code 3pvo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 40 binding sites of Calcium where determined in the Monoclinic Form of Human C-Reactive Protein, PDB code: 3pvo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 40 in 3pvo

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Calcium binding site 1 out of 40 in the Monoclinic Form of Human C-Reactive Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Monoclinic Form of Human C-Reactive Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5001

b:20.9
occ:1.00
 OD1 A:ASP140 2.2 21.9 1.0
OE1 A:GLU138 2.5 18.8 1.0
OD1 A:ASN61 2.5 20.3 1.0
OE2 A:GLU138 2.5 17.9 1.0
OD2 A:ASP60 2.6 20.0 1.0
O A:GLN139 2.6 19.3 1.0
CD A:GLU138 2.8 17.6 1.0
ND2 A:ASN61 3.2 19.0 1.0
CG A:ASN61 3.2 18.9 1.0
CG A:ASP140 3.4 20.9 1.0
C A:GLN139 3.7 19.3 1.0
CG A:ASP60 3.8 21.1 1.0
CA A:ASP140 4.0 20.2 1.0
N A:ASP140 4.2 19.7 1.0
OD2 A:ASP140 4.2 20.8 1.0
CB A:ASP140 4.3 20.1 1.0
CG A:GLU138 4.3 16.7 1.0
CB A:ASP60 4.6 21.3 1.0
OD1 A:ASP60 4.7 21.7 1.0
CB A:ASN61 4.7 18.9 1.0
N A:GLN139 4.9 18.5 1.0
CA A:GLN139 4.9 18.8 1.0

Calcium binding site 2 out of 40 in 3pvo

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Calcium binding site 2 out of 40 in the Monoclinic Form of Human C-Reactive Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Monoclinic Form of Human C-Reactive Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5002

b:62.0
occ:1.00
 OE2 A:GLU147 2.4 33.1 1.0
O A:GLU138 2.9 18.0 1.0
CD A:GLU147 3.1 31.8 1.0
OE1 A:GLN150 3.2 18.9 1.0
OE1 A:GLU138 3.2 18.8 1.0
N A:GLU147 3.4 22.9 1.0
OD2 A:ASP140 3.4 20.8 1.0
O A:ASN145 3.4 22.1 1.0
CG A:GLU147 3.5 27.3 1.0
CB A:GLU147 3.5 24.0 1.0
CG A:ASP140 3.7 20.9 1.0
C A:GLU138 3.7 17.7 1.0
CB A:GLU138 3.8 16.6 1.0
C A:PHE146 3.9 22.6 1.0
OD1 A:ASP140 4.0 21.9 1.0
CA A:PHE146 4.0 22.4 1.0
CA A:GLU147 4.0 23.5 1.0
OE1 A:GLU147 4.1 32.2 1.0
CD A:GLU138 4.1 17.6 1.0
N A:ASP140 4.3 19.7 1.0
CB A:ASP140 4.3 20.1 1.0
CA A:GLU138 4.3 16.9 1.0
CD A:GLN150 4.4 17.5 1.0
C A:ASN145 4.4 22.1 1.0
C A:GLN139 4.4 19.3 1.0
CG A:GLU138 4.5 16.7 1.0
N A:GLN139 4.6 18.5 1.0
O A:PHE146 4.7 22.8 1.0
N A:PHE146 4.7 22.3 1.0
O A:GLN139 4.8 19.3 1.0
N A:GLU138 4.8 16.4 1.0
CA A:ASP140 4.9 20.2 1.0
CA A:GLN139 4.9 18.8 1.0
O A:GLU147 4.9 22.8 1.0

Calcium binding site 3 out of 40 in 3pvo

Go back to Calcium Binding Sites List in 3pvo
Calcium binding site 3 out of 40 in the Monoclinic Form of Human C-Reactive Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Monoclinic Form of Human C-Reactive Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5004

b:55.3
occ:1.00
 OE1 B:GLU138 2.3 21.7 1.0
OD1 B:ASP140 2.6 21.5 1.0
OD2 B:ASP140 2.6 20.6 1.0
OE1 B:GLN150 2.7 17.3 1.0
CG B:ASP140 3.0 20.0 1.0
OE1 B:GLU147 3.3 30.0 1.0
NE2 B:GLN150 3.3 17.5 1.0
CD B:GLN150 3.4 17.5 1.0
CD B:GLU138 3.5 18.9 1.0
CA B:CA5006 3.6 34.5 1.0
CD B:GLU147 4.0 28.2 1.0
OE2 B:GLU138 4.2 18.4 1.0
CG B:GLU147 4.4 24.8 1.0
CG B:GLU138 4.4 16.5 1.0
CB B:ASP140 4.6 19.0 1.0
CB B:GLU138 4.8 15.8 1.0
CG B:GLN150 4.8 17.3 1.0
OE2 B:GLU147 4.9 29.2 1.0
O B:GLN139 5.0 17.5 1.0

Calcium binding site 4 out of 40 in 3pvo

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Calcium binding site 4 out of 40 in the Monoclinic Form of Human C-Reactive Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Monoclinic Form of Human C-Reactive Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5006

b:34.5
occ:1.00
 OE2 B:GLU138 2.1 18.4 1.0
O B:GLN139 2.1 17.5 1.0
OD2 B:ASP60 2.4 20.1 1.0
OD2 B:ASP140 2.4 20.6 1.0
OD1 B:ASN61 2.5 14.5 1.0
OE1 B:GLU138 2.6 21.7 1.0
CD B:GLU138 2.7 18.9 1.0
CG B:ASP140 3.2 20.0 1.0
C B:GLN139 3.2 17.5 1.0
CG B:ASN61 3.4 15.0 1.0
ND2 B:ASN61 3.5 15.6 1.0
CG B:ASP60 3.5 19.7 1.0
CA B:CA5004 3.6 55.3 1.0
CA B:ASP140 3.7 19.0 1.0
OD1 B:ASP140 3.8 21.5 1.0
N B:ASP140 3.9 18.1 1.0
CB B:ASP140 4.0 19.0 1.0
CG B:GLU138 4.2 16.5 1.0
CB B:ASP60 4.3 19.1 1.0
CA B:GLN139 4.4 17.1 1.0
N B:GLN139 4.4 16.6 1.0
OD1 B:ASP60 4.4 20.9 1.0
C B:ASP60 4.8 18.1 1.0
C B:GLU138 4.8 16.2 1.0
CB B:ASN61 4.8 16.0 1.0
O B:ASP60 4.8 17.7 1.0
N B:ASN61 4.9 17.0 1.0
C B:ASP140 5.0 19.1 1.0
O B:GLU138 5.0 16.6 1.0

Calcium binding site 5 out of 40 in 3pvo

Go back to Calcium Binding Sites List in 3pvo
Calcium binding site 5 out of 40 in the Monoclinic Form of Human C-Reactive Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Monoclinic Form of Human C-Reactive Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca5003

b:28.4
occ:1.00
 OE2 C:GLU138 2.1 15.4 1.0
OD2 C:ASP60 2.1 19.9 1.0
O C:GLN139 2.2 16.8 1.0
OD1 C:ASN61 2.4 19.7 1.0
OD1 C:ASP140 2.5 20.9 1.0
CD C:GLU138 2.9 16.7 1.0
OE1 C:GLU138 3.1 18.9 1.0
O C:HOH207 3.2 2.0 1.0
CG C:ASP60 3.3 19.2 1.0
CG C:ASN61 3.3 18.0 1.0
C C:GLN139 3.4 16.9 1.0
ND2 C:ASN61 3.5 19.7 1.0
CG C:ASP140 3.6 19.3 1.0
CA C:ASP140 3.7 17.8 1.0
N C:ASP140 3.9 17.4 1.0
CB C:ASP60 4.1 18.4 1.0
OD1 C:ASP60 4.1 20.4 1.0
CB C:ASP140 4.2 18.0 1.0
CA C:CA5005 4.2 32.5 1.0
O C:ASP60 4.3 17.8 1.0
CG C:GLU138 4.3 15.5 1.0
O C:HOH292 4.4 2.0 1.0
C C:ASP60 4.4 17.8 1.0
OD2 C:ASP140 4.6 20.9 1.0
CA C:GLN139 4.6 16.4 1.0
CB C:ASN61 4.7 16.6 1.0
N C:ASN61 4.7 17.1 1.0
N C:GLN139 4.8 16.0 1.0
C C:ASP140 4.8 17.7 1.0
CA C:ASP60 4.9 18.3 1.0

Calcium binding site 6 out of 40 in 3pvo

Go back to Calcium Binding Sites List in 3pvo
Calcium binding site 6 out of 40 in the Monoclinic Form of Human C-Reactive Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Monoclinic Form of Human C-Reactive Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca5005

b:32.5
occ:1.00
 OE1 C:GLU138 2.0 18.9 1.0
OE1 C:GLN150 2.2 13.0 1.0
OD2 C:ASP140 2.4 20.9 1.0
OE2 C:GLU147 2.4 25.9 1.0
OD1 C:ASP140 2.4 20.9 1.0
CG C:ASP140 2.7 19.3 1.0
CD C:GLU138 3.3 16.7 1.0
CD C:GLU147 3.3 25.0 1.0
O C:HOH207 3.4 2.0 1.0
CD C:GLN150 3.4 12.8 1.0
CG C:GLU147 3.6 20.9 1.0
O C:GLU138 3.8 15.8 1.0
NE2 C:GLN150 4.0 13.1 1.0
OE2 C:GLU138 4.1 15.4 1.0
CB C:ASP140 4.1 18.0 1.0
CB C:GLU138 4.1 15.2 1.0
CG C:GLU138 4.2 15.5 1.0
CB C:GLU147 4.2 18.1 1.0
CA C:CA5003 4.2 28.4 1.0
OE1 C:GLU147 4.4 27.2 1.0
C C:GLU138 4.5 15.7 1.0
O C:ASN145 4.5 17.2 1.0
O C:GLN139 4.6 16.8 1.0
CG C:GLN150 4.6 13.3 1.0
C C:GLN139 4.8 16.9 1.0
N C:ASP140 4.8 17.4 1.0
CA C:ASP140 4.8 17.8 1.0
N C:GLU147 4.8 17.1 1.0
CA C:GLU138 5.0 15.2 1.0

Calcium binding site 7 out of 40 in 3pvo

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Calcium binding site 7 out of 40 in the Monoclinic Form of Human C-Reactive Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Monoclinic Form of Human C-Reactive Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca5007

b:25.9
occ:1.00
 OE2 D:GLU138 2.1 22.7 1.0
OD1 D:ASP140 2.2 20.9 1.0
OD1 D:ASN61 2.7 20.4 1.0
CD D:GLU138 2.7 22.6 1.0
OE1 D:GLU138 2.7 24.2 1.0
OD2 D:ASP60 3.0 22.6 1.0
O D:GLN139 3.0 20.3 1.0
ND2 D:ASN61 3.2 19.7 1.0
CG D:ASN61 3.3 19.4 1.0
CG D:ASP140 3.4 20.9 1.0
C D:GLN139 4.1 20.3 1.0
CG D:ASP60 4.1 22.4 1.0
OD2 D:ASP140 4.1 20.9 1.0
CG D:GLU138 4.2 19.7 1.0
CA D:ASP140 4.3 20.8 1.0
CB D:ASP140 4.5 20.6 1.0
N D:ASP140 4.6 20.5 1.0
CB D:ASN61 4.8 19.2 1.0
CA D:CA5008 4.8 49.4 1.0
CB D:ASP60 4.9 21.9 1.0
OD1 D:ASP60 4.9 23.7 1.0

Calcium binding site 8 out of 40 in 3pvo

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Calcium binding site 8 out of 40 in the Monoclinic Form of Human C-Reactive Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Monoclinic Form of Human C-Reactive Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca5008

b:49.4
occ:1.00
 O D:GLU138 2.7 19.0 1.0
OE1 D:GLU138 2.7 24.2 1.0
OD2 D:ASP140 2.9 20.9 1.0
OE1 D:GLN150 2.9 18.3 1.0
OE1 D:GLU147 3.1 27.4 1.0
CG D:ASP140 3.2 20.9 1.0
CG D:GLU147 3.3 24.4 1.0
OD1 D:ASP140 3.5 20.9 1.0
N D:GLU147 3.5 22.7 1.0
O D:ASN145 3.5 22.6 1.0
CD D:GLU147 3.5 26.5 1.0
C D:GLU138 3.6 18.9 1.0
CD D:GLU138 3.7 22.6 1.0
CB D:GLU138 3.7 18.5 1.0
CB D:GLU147 3.8 22.7 1.0
C D:PHE146 4.1 22.6 1.0
CD D:GLN150 4.1 17.7 1.0
CA D:PHE146 4.2 22.5 1.0
CB D:ASP140 4.2 20.6 1.0
CA D:GLU138 4.2 18.5 1.0
CA D:GLU147 4.2 22.5 1.0
CG D:GLU138 4.3 19.7 1.0
C D:GLN139 4.4 20.3 1.0
N D:ASP140 4.4 20.5 1.0
N D:GLN139 4.5 19.3 1.0
O D:GLN139 4.5 20.3 1.0
C D:ASN145 4.5 22.6 1.0
OE2 D:GLU138 4.6 22.7 1.0
OE2 D:GLU147 4.7 26.4 1.0
N D:GLU138 4.7 17.7 1.0
CA D:GLN139 4.8 19.8 1.0
N D:PHE146 4.8 22.6 1.0
CA D:ASP140 4.8 20.8 1.0
CA D:CA5007 4.8 25.9 1.0
CG D:GLN150 4.9 17.1 1.0
CB D:GLN150 4.9 16.7 1.0
O D:PHE146 5.0 22.7 1.0
O D:GLU147 5.0 21.8 1.0

Calcium binding site 9 out of 40 in 3pvo

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Calcium binding site 9 out of 40 in the Monoclinic Form of Human C-Reactive Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Monoclinic Form of Human C-Reactive Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca5009

b:23.3
occ:1.00
 O E:GLN139 1.9 22.1 1.0
OD1 E:ASN61 2.1 20.6 1.0
OD2 E:ASP60 2.4 25.7 1.0
OE2 E:GLU138 2.5 22.6 1.0
OD1 E:ASP140 2.6 26.4 1.0
C E:GLN139 3.0 22.5 1.0
O E:HOH209 3.0 2.0 1.0
CG E:ASN61 3.1 20.8 1.0
CD E:GLU138 3.2 23.0 1.0
OE1 E:GLU138 3.3 23.4 1.0
CG E:ASP60 3.3 23.8 1.0
CA E:ASP140 3.4 23.7 1.0
ND2 E:ASN61 3.5 22.3 1.0
N E:ASP140 3.6 23.0 1.0
CG E:ASP140 3.6 25.0 1.0
CB E:ASP60 3.7 22.9 1.0
CB E:ASP140 4.0 23.7 1.0
O E:ASP60 4.0 22.3 1.0
C E:ASP60 4.1 22.3 1.0
CA E:GLN139 4.3 22.2 1.0
OD1 E:ASP60 4.3 24.0 1.0
N E:ASN61 4.4 21.5 1.0
CA E:CA5010 4.4 80.3 1.0
N E:GLN139 4.5 22.0 1.0
C E:ASP140 4.5 23.8 1.0
CB E:ASN61 4.5 20.5 1.0
CA E:ASP60 4.5 22.8 1.0
OD2 E:ASP140 4.6 26.3 1.0
CG E:GLU138 4.7 22.1 1.0
CA E:ASN61 4.8 20.5 1.0
CB E:GLN139 4.9 22.0 1.0

Calcium binding site 10 out of 40 in 3pvo

Go back to Calcium Binding Sites List in 3pvo
Calcium binding site 10 out of 40 in the Monoclinic Form of Human C-Reactive Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Monoclinic Form of Human C-Reactive Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca5010

b:80.3
occ:1.00
 OE1 E:GLN150 2.5 24.3 1.0
OE1 E:GLU147 2.5 33.6 1.0
OE1 E:GLU138 2.5 23.4 1.0
OD2 E:ASP140 2.5 26.3 1.0
OD1 E:ASP140 2.5 26.4 1.0
CG E:ASP140 2.9 25.0 1.0
O E:HOH209 3.1 2.0 1.0
CD E:GLN150 3.4 23.9 1.0
NE2 E:GLN150 3.5 24.3 1.0
CD E:GLU138 3.6 23.0 1.0
CD E:GLU147 3.7 33.6 1.0
CB E:ASP140 4.4 23.7 1.0
CG E:GLU147 4.4 31.0 1.0
OE2 E:GLU138 4.4 22.6 1.0
CA E:CA5009 4.4 23.3 1.0
CG E:GLU138 4.4 22.1 1.0
OE2 E:GLU147 4.6 34.0 1.0
CG E:GLN150 4.8 23.4 1.0
CB E:GLU138 4.9 21.4 1.0

Reference:

C.Guillon, U.M.Bigouagou, C.Folio, P.Jeannin, Y.Delneste, P.Gouet. A Staggered Decameric Assembly of Human C-Reactive Protein Stabilized By Zinc Ions Revealed By X-Ray Crystallography. Protein Pept.Lett. V. 22 248 2014.
ISSN: ISSN 0929-8665
PubMed: 25552313
Page generated: Sat Jul 13 16:58:01 2024

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