Calcium in PDB 2ux1: Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein

The structure of Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein, PDB code: 2ux1 was solved by H.Havukainen, A.Kauko, A.T.Pulliainen, S.Haataja, W.Meyer-Klaucke, J.Finne, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.520, 137.690, 142.060, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.8

The structure of Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	24 atoms

The binding sites of Calcium atom in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein (pdb code 2ux1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein, PDB code: 2ux1:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca173 b:18.4 occ:0.50 O D:HOH2077 2.2 33.1 1.0 O D:HOH2076 2.4 37.1 1.0 O D:HOH2082 2.5 36.3 1.0 O G:HOH2083 2.7 39.5 1.0 O D:ASN108 4.5 31.2 1.0 CA D:ASN108 4.7 30.2 1.0 O D:TYR107 4.8 27.1 1.0 O D:ARG51 4.8 26.2 1.0 C D:ASN108 4.8 30.6 1.0 O D:VAL109 4.9 29.5 1.0 O G:GLY167 4.9 30.2 1.0

Calcium binding site 2 out of 4 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca174 b:23.2 occ:0.50 O H:HOH2013 2.5 30.1 1.0 O K:HOH2089 2.5 37.2 1.0 O H:ASN108 2.8 36.0 1.0 C H:ASN108 3.9 35.7 1.0 CA H:ASN108 4.3 36.2 1.0 O H:VAL109 4.5 34.3 1.0 O K:GLY167 4.7 29.7 1.0 O H:TYR107 4.7 35.0 1.0 C H:VAL109 4.8 34.1 1.0 CL H:CL173 4.9 44.0 1.0 CG2 H:THR110 4.9 33.3 1.0 CA H:THR110 4.9 33.8 1.0 N H:THR110 5.0 33.9 1.0 ND2 H:ASN108 5.0 41.6 1.0

Calcium binding site 3 out of 4 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca174 b:38.4 occ:1.00 O I:HOH2056 2.3 32.4 1.0 O I:HOH2053 2.4 34.2 1.0 O D:HOH2121 2.6 42.6 1.0 O I:HOH2054 2.6 37.3 1.0 O I:ASN108 4.2 33.0 1.0 O I:TYR107 4.5 29.7 1.0 O I:ARG51 4.6 29.1 1.0 CA I:ASN108 4.6 32.8 1.0 C I:ASN108 4.7 32.9 1.0 O D:GLY167 4.7 27.0 1.0 O I:VAL109 4.7 33.1 1.0 O I:HOH2058 4.9 20.1 1.0

Calcium binding site 4 out of 4 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein within 5.0Å range: probe atom residue distance (Å) B Occ K:Ca174 b:30.4 occ:1.00 O K:HOH2076 2.2 36.8 1.0 OD2 K:ASP24 2.2 36.0 1.0 OE2 K:GLU139 2.3 30.1 1.0 O K:HOH2075 2.3 32.4 1.0 CD K:GLU139 3.3 32.4 1.0 CG K:ASP24 3.4 35.0 1.0 CG K:GLU139 3.7 31.8 1.0 CB K:ASP24 3.8 33.5 1.0 N K:ASP24 4.4 32.6 1.0 OE1 K:GLU139 4.4 31.7 1.0 OD1 K:ASP24 4.4 35.6 1.0 CA K:ASP24 4.8 32.7 1.0

H.Havukainen, S.Haataja, A.Kauko, A.T.Pulliainen, A.Salminen, T.Haikarainen, J.Finne, A.C.Papageorgiou. Structural Basis of the Zinc- and Terbium-Mediated Inhibition of Ferroxidase Activity in Dps Ferritin- Like Proteins. Protein Sci. V. 17 1513 2008.
ISSN: ISSN 0961-8368
PubMed: 18552126
DOI: 10.1110/PS.036236.108