Zinc 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:

Calcium

(Ca)

40 atoms

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc, PDB code: 3pvn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn6001 b:39.5 occ:1.00 NE2 A:HIS38 2.3 18.1 1.0 O A:HOH2754 2.3 20.5 1.0 O A:HOH1742 2.3 32.1 1.0 O A:HOH3098 2.5 52.0 1.0 O T:HOH1822 2.7 30.4 1.0 CD2 A:HIS38 3.1 12.8 1.0 CE1 A:HIS38 3.3 16.9 1.0 O A:PRO206 3.8 24.9 1.0 O A:TYR175 3.8 11.0 1.0 CG A:HIS38 4.3 12.5 1.0 ND1 A:HIS95 4.4 12.0 1.0 ND1 A:HIS38 4.4 16.3 1.0 O A:ILE174 4.5 15.4 1.0 CD1 A:TRP205 4.7 13.9 1.0 C A:TYR175 4.8 13.5 1.0 OD1 A:ASN158 4.9 29.5 1.0 O T:HOH3013 4.9 52.9 1.0 CE1 A:HIS95 4.9 9.5 1.0 CG A:HIS95 5.0 10.0 1.0 O A:HOH557 5.0 22.5 1.0 C A:PRO206 5.0 23.9 1.0

Zinc binding site 2 out of 5 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 G:Zn6002 b:57.4 occ:1.00 NE2 G:HIS38 2.4 21.7 1.0 O G:HOH3100 2.5 47.7 1.0 O M:HOH2761 2.6 37.5 1.0 O G:HOH3099 2.8 57.1 1.0 CD2 G:HIS38 3.0 19.7 1.0 O G:HOH2525 3.2 31.7 1.0 CE1 G:HIS38 3.6 17.5 1.0 O G:PRO206 3.7 26.0 1.0 O G:TYR175 3.9 15.7 1.0 CG G:HIS38 4.3 18.6 1.0 ND1 G:HIS95 4.4 18.4 1.0 O G:ILE174 4.4 17.2 1.0 OD1 G:ASN158 4.5 25.9 1.0 ND1 G:HIS38 4.5 18.9 1.0 CD1 G:TRP205 4.7 18.3 1.0 O G:HOH2513 4.8 33.2 1.0 C G:TYR175 4.8 16.8 1.0 C G:PRO206 4.9 26.9 1.0 O G:HOH2121 4.9 45.2 1.0 CE1 G:HIS95 4.9 10.8 1.0 OG M:SER181 4.9 27.4 1.0 CG G:ASN158 5.0 20.5 1.0

Zinc binding site 3 out of 5 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 L:Zn6003 b:43.4 occ:1.00 NE2 L:HIS38 2.3 20.6 1.0 O L:HOH2771 2.3 29.9 1.0 O L:HOH2799 2.4 33.2 1.0 O L:HOH3101 2.4 47.4 1.0 O H:HOH677 2.7 26.0 1.0 CD2 L:HIS38 3.2 17.6 1.0 CE1 L:HIS38 3.4 17.4 1.0 O L:PRO206 3.7 30.3 1.0 O L:TYR175 3.9 15.2 1.0 O L:HOH1321 4.3 32.3 1.0 CG L:HIS38 4.4 17.1 1.0 ND1 L:HIS38 4.4 14.9 1.0 O H:HOH2643 4.5 47.2 1.0 ND1 L:HIS95 4.6 14.7 1.0 O L:ILE174 4.6 15.4 1.0 CD1 L:TRP205 4.7 11.8 1.0 C L:PRO206 4.9 28.6 1.0 OD1 L:ASN158 4.9 24.6 1.0 OG H:SER181 4.9 23.9 1.0 C L:TYR175 4.9 16.8 1.0

Zinc binding site 4 out of 5 in the Triclinic Form of Human C-Reactive Protein in Complex with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 S:Zn6004 b:44.0 occ:1.00 NE2 S:HIS38 2.2 20.6 1.0 O S:HOH2692 2.2 31.1 1.0 O S:HOH1430 2.4 23.6 1.0 O S:HOH3050 2.5 33.5 1.0 O S:HOH2486 2.5 33.2 1.0 O B:HOH614 2.8 22.0 1.0 CD2 S:HIS38 2.9 20.5 1.0 CE1 S:HIS38 3.4 17.2 1.0 O S:PRO206 3.8 26.1 1.0 O S:TYR175 3.9 15.8 1.0 CG S:HIS38 4.2 17.7 1.0 ND1 S:HIS38 4.4 21.3 1.0 ND1 S:HIS95 4.4 18.8 1.0 O S:ILE174 4.6 16.7 1.0 O S:HOH947 4.6 37.4 1.0 CD1 S:TRP205 4.7 12.8 1.0 O S:HOH1577 4.7 28.9 1.0 C S:TYR175 4.9 16.5 1.0 CE1 S:HIS95 4.9 14.7 1.0 ND2 S:ASN158 4.9 23.2 1.0 CG S:HIS95 5.0 14.6 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 T:Zn6005 b:26.6 occ:1.00 OD1 T:ASP60 2.0 12.7 1.0 O T:HOH3102 2.1 19.6 1.0 CG T:ASP60 2.8 9.5 1.0 OD2 T:ASP60 2.8 12.0 1.0 O T:HOH1450 3.6 40.4 1.0 NE2 T:GLN59 4.0 11.5 1.0 CB T:ASP60 4.3 9.2 1.0 CG T:ASN61 4.4 13.1 1.0 ND2 T:ASN61 4.4 19.8 1.0 OD1 T:ASN61 4.4 16.0 1.0 N T:ASP60 4.7 9.2 1.0 CA T:CA5040 4.7 13.8 1.0 N T:ASN61 4.8 9.0 1.0 O T:HOH3094 4.8 34.8 1.0 CA T:ASP60 4.9 9.7 1.0 CB T:ASN61 5.0 10.7 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