Calcium in PDB 3pvn: Triclinic Form of Human C-Reactive Protein in Complex with Zinc

The structure of Triclinic Form of Human C-Reactive Protein in Complex with Zinc, PDB code: 3pvn 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)	19.92 / 1.98
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	79.300, 96.400, 160.400, 79.90, 77.10, 69.40
R / Rfree (%)	17.6 / 23.6

The structure of Triclinic Form of Human C-Reactive Protein in Complex with Zinc also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

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

Calcium binding site 1 out of 40 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Triclinic Form of Human C-Reactive Protein in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5001 b:32.3 occ:1.00 O A:GLN139 2.4 22.8 1.0 OE1 A:GLU138 2.4 23.2 1.0 OD1 A:ASP140 2.5 25.6 1.0 OD1 A:ASN61 2.5 22.5 1.0 OE2 A:GLU138 2.7 27.9 1.0 OD2 A:ASP60 2.7 31.7 1.0 CD A:GLU138 2.9 30.3 1.0 O A:HOH351 3.3 28.7 1.0 CG A:ASN61 3.4 22.1 1.0 C A:GLN139 3.4 23.5 1.0 ND2 A:ASN61 3.5 23.5 1.0 CG A:ASP140 3.6 24.3 1.0 CG A:ASP60 3.7 24.4 1.0 CA A:ASP140 3.8 25.8 1.0 CA A:CA5002 3.9 43.7 1.0 N A:ASP140 4.0 25.7 1.0 CB A:ASP60 4.1 21.8 1.0 CB A:ASP140 4.4 26.4 1.0 CG A:GLU138 4.4 23.4 1.0 O A:HOH772 4.5 21.5 1.0 CA A:GLN139 4.6 23.0 1.0 OD2 A:ASP140 4.6 24.8 1.0 N A:GLN139 4.7 21.9 1.0 C A:ASP60 4.7 20.9 1.0 OD1 A:ASP60 4.7 28.8 1.0 CB A:ASN61 4.8 17.9 1.0 O A:ASP60 4.9 21.6 1.0 N A:ASN61 4.9 19.7 1.0 C A:GLU138 5.0 22.4 1.0

Calcium binding site 2 out of 40 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Triclinic Form of Human C-Reactive Protein in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5002 b:43.7 occ:1.00 OE1 A:GLN150 2.4 23.1 1.0 OE1 A:GLU138 2.5 23.2 1.0 OD2 A:ASP140 2.6 24.8 1.0 OE1 A:GLU147 2.6 42.0 1.0 O A:HOH288 2.6 21.0 1.0 OD1 A:ASP140 2.7 25.6 1.0 CG A:ASP140 3.0 24.3 1.0 CD A:GLN150 3.4 22.9 1.0 O A:HOH351 3.5 28.7 1.0 NE2 A:GLN150 3.7 27.2 1.0 CD A:GLU147 3.7 41.7 1.0 CD A:GLU138 3.7 30.3 1.0 CA A:CA5001 3.9 32.3 1.0 CG A:GLU147 4.0 34.3 1.0 O A:GLU138 4.1 22.7 1.0 CB A:ASP140 4.3 26.4 1.0 CB A:GLU138 4.3 20.5 1.0 CG A:GLU138 4.3 23.4 1.0 CB A:GLU147 4.5 27.9 1.0 C A:GLU138 4.7 22.4 1.0 OE2 A:GLU138 4.7 27.9 1.0 O A:HOH1885 4.7 31.2 1.0 OE2 A:GLU147 4.8 45.3 1.0 CG A:GLN150 4.8 22.4 1.0 O A:GLN139 4.8 22.8 1.0 N A:ASP140 4.8 25.7 1.0 C A:GLN139 4.9 23.5 1.0 CA A:ASP140 4.9 25.8 1.0 O A:ASN145 4.9 28.9 1.0

Calcium binding site 3 out of 40 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Triclinic Form of Human C-Reactive Protein in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5003 b:22.8 occ:1.00 O B:HOH208 2.3 12.5 1.0 OE1 B:GLU147 2.3 24.6 1.0 OE1 B:GLN150 2.4 17.5 1.0 OE1 B:GLU138 2.4 17.2 1.0 OD1 B:ASP140 2.4 21.3 1.0 OD2 B:ASP140 2.7 17.4 1.0 CG B:ASP140 2.8 23.1 1.0 CD B:GLN150 3.3 15.6 1.0 CD B:GLU147 3.4 28.2 1.0 CD B:GLU138 3.5 22.5 1.0 NE2 B:GLN150 3.6 21.1 1.0 CG B:GLU147 3.8 21.2 1.0 CA B:CA5004 3.9 29.6 1.0 CB B:ASP140 4.2 22.4 1.0 CG B:GLU138 4.3 15.1 1.0 CB B:GLU138 4.4 14.9 1.0 OE2 B:GLU138 4.4 21.8 1.0 OE2 B:GLU147 4.4 33.8 1.0 CB B:GLU147 4.5 18.5 1.0 O B:HOH681 4.5 17.4 1.0 O B:GLU138 4.6 18.1 1.0 O B:GLN139 4.7 18.1 1.0 CG B:GLN150 4.7 17.3 1.0 O B:ASN145 4.8 18.6 1.0 N B:ASP140 4.8 20.6 1.0 C B:GLN139 4.8 19.3 1.0 C B:GLU138 4.9 17.6 1.0 CA B:ASP140 4.9 22.1 1.0

Calcium binding site 4 out of 40 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Triclinic Form of Human C-Reactive Protein in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5004 b:29.6 occ:1.00 OD2 B:ASP140 2.3 17.4 1.0 O B:GLN139 2.3 18.1 1.0 OD1 B:ASN61 2.5 17.7 1.0 OE2 B:GLU138 2.5 21.8 1.0 OD2 B:ASP60 2.6 28.0 1.0 OE1 B:GLU138 2.7 17.2 1.0 CD B:GLU138 3.0 22.5 1.0 CG B:ASN61 3.3 16.7 1.0 ND2 B:ASN61 3.4 19.1 1.0 C B:GLN139 3.4 19.3 1.0 CG B:ASP140 3.5 23.1 1.0 CG B:ASP60 3.6 26.3 1.0 CA B:ASP140 3.8 22.1 1.0 CA B:CA5003 3.9 22.8 1.0 N B:ASP140 4.0 20.6 1.0 O B:HOH582 4.2 19.0 1.0 CB B:ASP140 4.2 22.4 1.0 CB B:ASP60 4.3 22.4 1.0 OD1 B:ASP140 4.4 21.3 1.0 CG B:GLU138 4.5 15.1 1.0 OD1 B:ASP60 4.5 30.9 1.0 CA B:GLN139 4.7 19.1 1.0 N B:GLN139 4.7 18.7 1.0 CB B:ASN61 4.8 15.9 1.0 C B:ASP60 4.9 20.1 1.0 N B:ASN61 4.9 18.0 1.0 O B:HOH733 5.0 34.0 1.0

Calcium binding site 5 out of 40 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Triclinic Form of Human C-Reactive Protein in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca5005 b:66.7 occ:1.00 OE1 C:GLN150 2.6 26.4 1.0 OE1 C:GLU138 2.6 33.6 1.0 OE2 C:GLU147 2.7 46.6 1.0 OD2 C:ASP140 2.8 30.3 1.0 OD1 C:ASP140 2.8 24.6 1.0 O C:HOH1631 2.9 45.7 1.0 CG C:ASP140 3.1 27.7 1.0 CD C:GLN150 3.5 25.5 1.0 CD C:GLU147 3.6 47.5 1.0 NE2 C:GLN150 3.8 28.7 1.0 CD C:GLU138 3.8 31.9 1.0 CA C:CA5006 4.1 32.8 1.0 OE1 C:GLU147 4.3 49.2 1.0 CG C:GLU147 4.4 39.5 1.0 CB C:GLU138 4.5 22.4 1.0 CG C:GLU138 4.5 23.7 1.0 CB C:GLU147 4.6 32.7 1.0 O C:GLU138 4.6 21.9 1.0 CB C:ASP140 4.6 27.4 1.0 O C:HOH2270 4.7 46.2 1.0 OE2 C:GLU138 4.8 29.8 1.0 CG C:GLN150 4.9 23.5 1.0

Calcium binding site 6 out of 40 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Triclinic Form of Human C-Reactive Protein in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca5006 b:32.8 occ:1.00 OD2 C:ASP60 2.3 30.8 1.0 O C:GLN139 2.3 22.6 1.0 OD1 C:ASN61 2.5 31.6 1.0 OE2 C:GLU138 2.5 29.8 1.0 OD1 C:ASP140 2.5 24.6 1.0 OE1 C:GLU138 2.7 33.6 1.0 CD C:GLU138 2.9 31.9 1.0 C C:GLN139 3.3 23.8 1.0 CG C:ASP60 3.5 31.7 1.0 CG C:ASN61 3.5 30.2 1.0 CG C:ASP140 3.7 27.7 1.0 ND2 C:ASN61 3.8 31.8 1.0 CA C:ASP140 3.8 27.3 1.0 N C:ASP140 3.9 25.3 1.0 CB C:ASP60 4.0 28.3 1.0 CA C:CA5005 4.1 66.7 1.0 O C:HOH240 4.2 19.2 1.0 CB C:ASP140 4.4 27.4 1.0 CG C:GLU138 4.4 23.7 1.0 CA C:GLN139 4.4 23.1 1.0 N C:GLN139 4.5 22.3 1.0 OD1 C:ASP60 4.5 36.1 1.0 O C:HOH2757 4.5 46.5 1.0 C C:ASP60 4.5 26.7 1.0 O C:ASP60 4.6 25.6 1.0 OD2 C:ASP140 4.6 30.3 1.0 N C:ASN61 4.7 25.4 1.0 C C:GLU138 4.8 22.1 1.0 CB C:ASN61 4.8 25.5 1.0 CA C:ASP60 4.9 27.7 1.0 C C:ASP140 4.9 28.2 1.0

Calcium binding site 7 out of 40 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Triclinic Form of Human C-Reactive Protein in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca5007 b:15.7 occ:1.00 OD2 D:ASP60 2.3 15.8 1.0 O D:GLN139 2.3 13.9 1.0 OD1 D:ASN61 2.4 12.4 1.0 OD1 D:ASP140 2.5 17.1 1.0 OE2 D:GLU138 2.5 19.6 1.0 OE1 D:GLU138 2.7 18.1 1.0 CD D:GLU138 2.9 18.7 1.0 C D:GLN139 3.3 13.4 1.0 CG D:ASN61 3.4 14.1 1.0 CG D:ASP60 3.4 15.8 1.0 CG D:ASP140 3.7 21.4 1.0 ND2 D:ASN61 3.7 11.5 1.0 CA D:ASP140 3.8 16.5 1.0 N D:ASP140 3.9 13.9 1.0 CB D:ASP60 3.9 13.5 1.0 O D:HOH209 4.1 14.4 1.0 O D:HOH1761 4.2 19.0 1.0 O D:ASP60 4.3 9.4 1.0 CB D:ASP140 4.4 17.6 1.0 C D:ASP60 4.4 11.4 1.0 CG D:GLU138 4.4 15.7 1.0 OD1 D:ASP60 4.5 17.6 1.0 CA D:CA5008 4.5 56.4 1.0 CA D:GLN139 4.5 14.0 1.0 N D:GLN139 4.5 13.1 1.0 O D:HOH1251 4.5 29.5 1.0 OD2 D:ASP140 4.6 23.2 1.0 N D:ASN61 4.7 9.5 1.0 CB D:ASN61 4.7 9.4 1.0 CA D:ASP60 4.9 11.6 1.0 C D:ASP140 4.9 16.2 1.0 C D:GLU138 4.9 13.6 1.0 CA D:ASN61 4.9 11.9 1.0

Calcium binding site 8 out of 40 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Triclinic Form of Human C-Reactive Protein in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca5008 b:56.4 occ:1.00 OE1 D:GLU138 2.6 18.1 1.0 O D:HOH2986 2.7 11.9 1.0 OE1 D:GLN150 2.8 14.7 1.0 O D:HOH432 2.9 32.6 1.0 O D:HOH1251 3.2 29.5 1.0 OD1 D:ASP140 3.5 17.1 1.0 OD2 D:ASP140 3.6 23.2 1.0 CD D:GLN150 3.6 22.0 1.0 O D:HOH1202 3.6 25.9 1.0 CD D:GLU138 3.7 18.7 1.0 CG D:ASP140 3.8 21.4 1.0 NE2 D:GLN150 3.9 20.8 1.0 CG D:GLU138 4.1 15.7 1.0 CB D:GLU138 4.1 12.3 1.0 CB D:GLU147 4.2 19.0 1.0 O D:HOH2898 4.3 38.7 1.0 CA D:CA5007 4.5 15.7 1.0 O D:GLU138 4.5 14.7 1.0 OE2 D:GLU138 4.7 19.6 1.0 CG D:GLN150 4.8 15.5 1.0 CG D:GLU147 4.9 20.4 1.0 CB D:ASP140 5.0 17.6 1.0 C D:GLU138 5.0 13.6 1.0

Calcium binding site 9 out of 40 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Triclinic Form of Human C-Reactive Protein in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca5009 b:25.2 occ:1.00 OE2 E:GLU138 2.3 25.2 1.0 OD1 E:ASP140 2.4 26.2 1.0 OD1 E:ASN61 2.4 19.7 1.0 O E:GLN139 2.5 19.7 1.0 OD2 E:ASP60 2.5 21.1 1.0 OE1 E:GLU138 2.6 20.4 1.0 O E:HOH367 2.8 27.7 1.0 CD E:GLU138 2.8 21.4 1.0 CG E:ASN61 3.4 19.6 1.0 C E:GLN139 3.4 19.6 1.0 CG E:ASP60 3.6 22.0 1.0 CG E:ASP140 3.6 24.4 1.0 ND2 E:ASN61 3.7 19.4 1.0 CA E:ASP140 3.8 21.6 1.0 CA E:CA5010 3.9 28.8 1.0 N E:ASP140 4.0 19.2 1.0 CB E:ASP60 4.2 18.7 1.0 CG E:GLU138 4.3 19.1 1.0 CB E:ASP140 4.3 20.9 1.0 O E:HOH265 4.3 21.2 1.0 OD1 E:ASP60 4.5 21.8 1.0 OD2 E:ASP140 4.6 27.4 1.0 O E:ASP60 4.6 17.9 1.0 N E:GLN139 4.6 18.4 1.0 CA E:GLN139 4.6 19.2 1.0 C E:ASP60 4.6 18.2 1.0 CB E:ASN61 4.8 18.8 1.0 N E:ASN61 4.9 18.1 1.0 C E:GLU138 5.0 17.7 1.0

Calcium binding site 10 out of 40 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Triclinic Form of Human C-Reactive Protein in Complex with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca5010 b:28.8 occ:1.00 OE1 E:GLN150 2.2 24.6 1.0 OE1 E:GLU147 2.3 26.5 1.0 OE1 E:GLU138 2.3 20.4 1.0 OD2 E:ASP140 2.6 27.4 1.0 OD1 E:ASP140 2.6 26.2 1.0 O E:HOH399 2.6 21.6 1.0 CG E:ASP140 2.9 24.4 1.0 CD E:GLN150 3.2 21.8 1.0 CD E:GLU147 3.3 30.1 1.0 NE2 E:GLN150 3.5 18.9 1.0 CD E:GLU138 3.5 21.4 1.0 O E:HOH367 3.6 27.7 1.0 CG E:GLU147 3.8 24.7 1.0 CA E:CA5009 3.9 25.2 1.0 CB E:GLU138 4.3 16.9 1.0 CB E:ASP140 4.3 20.9 1.0 CG E:GLU138 4.3 19.1 1.0 OE2 E:GLU147 4.4 37.4 1.0 OE2 E:GLU138 4.4 25.2 1.0 O E:GLU138 4.5 20.4 1.0 CB E:GLU147 4.6 23.0 1.0 CG E:GLN150 4.6 19.8 1.0 N E:ASP140 4.8 19.2 1.0 O E:ASN145 4.8 23.5 1.0 C E:GLU138 4.9 17.7 1.0 O E:GLN139 4.9 19.7 1.0 C E:GLN139 4.9 19.6 1.0 CA E:ASP140 4.9 21.6 1.0

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