Zinc 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
Calcium	(Ca)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc 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 Zinc atom.
In total 24 binding sites of Zinc where determined in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein, PDB code: 2ux1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 A:Zn1173 b:42.8 occ:1.00 ND1 A:HIS44 2.1 27.2 1.0 NE2 A:HIS40 2.1 34.3 1.0 O A:HOH2106 2.4 31.1 1.0 O A:HOH2105 2.5 37.3 1.0 CE1 A:HIS44 2.8 27.8 1.0 CD2 A:HIS40 2.9 31.9 1.0 CG A:HIS44 3.1 26.5 1.0 CE1 A:HIS40 3.2 33.9 1.0 CB A:HIS44 3.6 24.9 1.0 NE2 A:HIS44 4.0 29.2 1.0 CG A:HIS40 4.1 30.5 1.0 CD2 A:HIS44 4.1 27.5 1.0 ND1 A:HIS40 4.2 33.4 1.0 SD A:MET66 4.2 30.6 1.0 O A:HIS40 4.9 27.5 1.0 O C:HOH2029 4.9 42.7 1.0 CD2 C:LEU73 5.0 31.6 1.0 CA A:HIS44 5.0 23.8 1.0

Zinc binding site 2 out of 24 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 A:Zn1174 b:29.8 occ:1.00 OD2 A:ASP74 2.0 29.5 1.0 OE2 A:GLU78 2.1 29.7 1.0 NE2 C:HIS47 2.1 28.6 1.0 O A:HOH2107 2.1 23.4 1.0 O A:HOH2108 2.2 41.5 1.0 CG A:ASP74 2.7 29.3 1.0 OD1 A:ASP74 2.7 28.8 1.0 CD A:GLU78 3.0 31.0 1.0 CD2 C:HIS47 3.0 29.7 1.0 CE1 C:HIS47 3.1 29.2 1.0 OE1 A:GLU78 3.3 33.8 1.0 NE2 C:HIS59 4.0 29.6 1.0 CE1 C:HIS59 4.0 29.8 1.0 O A:HOH2033 4.1 36.5 1.0 CB A:ASP74 4.2 29.7 1.0 CG C:HIS47 4.2 29.1 1.0 ND1 C:HIS47 4.2 27.4 1.0 O C:HOH2019 4.3 41.5 1.0 CG A:GLU78 4.3 29.4 1.0 OD2 C:ASP63 4.5 38.6 1.0 OD1 C:ASP63 4.5 35.8 1.0 O E:HOH2071 4.5 50.4 1.0 NE1 C:TRP48 4.7 27.8 1.0 CG C:ASP63 4.9 33.2 1.0 CD1 C:TRP48 4.9 27.2 1.0

Zinc binding site 3 out of 24 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 B:Zn1173 b:23.5 occ:1.00 O B:HOH2096 1.4 20.7 1.0 OD2 B:ASP74 1.8 24.1 1.0 OE2 B:GLU78 2.0 15.0 1.0 NE2 D:HIS47 2.0 23.0 1.0 O B:HOH2097 2.1 18.2 1.0 CG B:ASP74 2.7 26.6 1.0 CD B:GLU78 2.9 24.1 1.0 OD1 B:ASP74 2.9 24.8 1.0 CE1 D:HIS47 3.0 24.1 1.0 CD2 D:HIS47 3.1 22.6 1.0 OE1 B:GLU78 3.2 24.5 1.0 NE2 D:HIS59 3.9 24.8 1.0 CE1 D:HIS59 4.0 22.1 1.0 ND1 D:HIS47 4.1 24.8 1.0 CB B:ASP74 4.2 27.2 1.0 CG D:HIS47 4.2 24.8 1.0 CG B:GLU78 4.2 22.0 1.0 OD2 D:ASP63 4.4 34.0 1.0 OD1 D:ASP63 4.4 33.8 1.0 O B:HOH2031 4.4 36.1 1.0 NE1 D:TRP48 4.5 21.8 1.0 CD1 D:TRP48 4.8 23.9 1.0 CG D:ASP63 4.8 28.4 1.0 CD2 D:HIS59 5.0 24.1 1.0 NE2 D:HIS44 5.0 28.2 1.0

Zinc binding site 4 out of 24 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 B:Zn1174 b:41.9 occ:1.00 ND1 B:HIS44 1.9 23.9 1.0 NE2 B:HIS40 2.3 29.2 1.0 O B:HOH2098 2.5 29.5 1.0 CE1 B:HIS44 2.8 25.1 1.0 CG B:HIS44 3.0 24.6 1.0 CD2 B:HIS40 3.1 27.7 1.0 CE1 B:HIS40 3.4 28.9 1.0 CB B:HIS44 3.5 21.7 1.0 NE2 B:HIS44 3.9 26.1 1.0 O D:HOH2010 4.0 33.6 1.0 CD2 B:HIS44 4.1 22.5 1.0 CD2 D:LEU73 4.1 27.6 1.0 O D:HOH2038 4.2 30.4 1.0 SD B:MET66 4.2 28.0 1.0 CG B:HIS40 4.3 25.5 1.0 ND1 B:HIS40 4.4 29.2 1.0 O B:HIS40 4.8 23.0 1.0 O D:HOH2036 4.9 43.3 1.0 CA B:HIS44 4.9 21.1 1.0

Zinc binding site 5 out of 24 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1173 b:25.3 occ:1.00 O C:HOH2086 1.7 28.1 1.0 OD2 C:ASP74 1.9 27.5 1.0 NE2 A:HIS47 2.1 23.4 1.0 OE2 C:GLU78 2.1 19.0 1.0 O C:HOH2085 2.1 21.8 1.0 CG C:ASP74 2.8 28.2 1.0 OD1 C:ASP74 2.9 29.6 1.0 CD C:GLU78 2.9 26.9 1.0 CD2 A:HIS47 3.0 23.8 1.0 CE1 A:HIS47 3.1 23.2 1.0 OE1 C:GLU78 3.2 27.0 1.0 NE2 A:HIS59 3.8 26.2 1.0 CE1 A:HIS59 4.0 24.6 1.0 ND1 A:HIS47 4.2 23.1 1.0 CG A:HIS47 4.2 24.8 1.0 CB C:ASP74 4.2 27.4 1.0 CG C:GLU78 4.2 23.2 1.0 O C:HOH2031 4.3 36.3 1.0 OD1 A:ASP63 4.3 28.7 0.5 O A:HOH2020 4.4 40.0 1.0 OD2 A:ASP63 4.4 28.7 0.5 NE1 A:TRP48 4.6 24.4 1.0 CG A:ASP63 4.8 27.4 0.5 CD1 A:TRP48 4.9 26.6 1.0 CD2 A:HIS59 4.9 24.3 1.0

Zinc binding site 6 out of 24 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1174 b:42.8 occ:1.00 ND1 C:HIS44 2.0 26.1 1.0 NE2 C:HIS40 2.1 33.9 1.0 O C:HOH2087 2.3 39.2 1.0 CE1 C:HIS44 2.8 27.7 1.0 CD2 C:HIS40 2.9 32.5 1.0 CG C:HIS44 3.1 26.4 1.0 CE1 C:HIS40 3.1 33.2 1.0 CB C:HIS44 3.5 26.1 1.0 O A:HOH2005 3.7 41.2 1.0 NE2 C:HIS44 4.0 28.1 1.0 CG C:HIS40 4.1 30.8 1.0 CD2 C:HIS44 4.1 27.9 1.0 ND1 C:HIS40 4.1 34.8 1.0 O A:HOH2030 4.3 37.8 1.0 SD C:MET66 4.3 29.1 1.0 CD2 A:LEU73 4.7 33.7 1.0 O C:HIS40 4.8 26.5 1.0 CD1 A:LEU73 4.9 34.5 1.0 CA C:HIS44 4.9 26.2 1.0

Zinc binding site 7 out of 24 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 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:Zn1173 b:44.5 occ:1.00 ND1 D:HIS44 2.1 27.9 1.0 O D:HOH2130 2.3 32.9 1.0 NE2 D:HIS40 2.3 32.1 1.0 O D:HOH2131 2.9 41.1 1.0 CD2 D:HIS40 3.0 32.3 1.0 CE1 D:HIS44 3.0 29.4 1.0 CG D:HIS44 3.1 24.7 1.0 CE1 D:HIS40 3.5 31.6 1.0 CB D:HIS44 3.5 24.1 1.0 O B:HOH2008 3.8 31.1 1.0 NE2 D:HIS44 4.1 28.2 1.0 CD2 D:HIS44 4.2 25.1 1.0 CG D:HIS40 4.2 27.7 1.0 O B:HOH2028 4.3 40.3 1.0 SD D:MET66 4.4 29.1 1.0 ND1 D:HIS40 4.4 30.9 1.0 O D:HIS40 4.7 25.7 1.0 CD2 B:LEU73 4.8 31.2 1.0 CA D:HIS44 5.0 23.3 1.0

Zinc binding site 8 out of 24 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 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:Zn1174 b:24.5 occ:1.00 O D:HOH2133 2.0 31.4 1.0 OD2 D:ASP74 2.0 23.5 1.0 OE2 D:GLU78 2.0 28.4 1.0 NE2 B:HIS47 2.1 20.7 1.0 O D:HOH2132 2.1 22.5 1.0 CG D:ASP74 2.7 23.4 1.0 OD1 D:ASP74 2.7 24.3 1.0 CD D:GLU78 3.0 27.1 1.0 CD2 B:HIS47 3.0 20.0 1.0 CE1 B:HIS47 3.1 19.9 1.0 OE1 D:GLU78 3.3 28.2 1.0 NE2 B:HIS59 3.9 24.0 1.0 CE1 B:HIS59 3.9 23.2 1.0 ND1 B:HIS47 4.2 21.1 1.0 CB D:ASP74 4.2 24.0 1.0 CG B:HIS47 4.2 19.9 1.0 O B:HOH2020 4.3 32.2 1.0 CG D:GLU78 4.3 23.5 1.0 OD1 B:ASP63 4.3 34.1 1.0 O F:HOH2095 4.4 29.2 1.0 OD2 B:ASP63 4.4 34.4 1.0 NE1 B:TRP48 4.7 19.2 1.0 CG B:ASP63 4.8 30.4 1.0 CD1 B:TRP48 4.9 19.6 1.0 O D:ASP74 4.9 25.3 1.0 CD2 B:HIS59 5.0 22.1 1.0

Zinc binding site 9 out of 24 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1173 b:32.0 occ:1.00 OD2 E:ASP74 2.0 31.9 1.0 OE2 E:GLU78 2.0 28.4 1.0 NE2 G:HIS47 2.1 25.1 1.0 O E:HOH2081 2.1 42.9 1.0 O E:HOH2082 2.1 38.3 1.0 CG E:ASP74 2.9 31.0 1.0 CE1 G:HIS47 2.9 26.7 1.0 CD E:GLU78 3.0 32.5 1.0 OD1 E:ASP74 3.0 30.2 1.0 CD2 G:HIS47 3.2 27.5 1.0 OE1 E:GLU78 3.4 32.2 1.0 O G:HOH2026 3.8 45.8 1.0 NE2 G:HIS59 3.8 28.6 1.0 CE1 G:HIS59 4.0 28.9 1.0 ND1 G:HIS47 4.1 26.7 1.0 CG G:HIS47 4.2 26.4 1.0 OD2 G:ASP63 4.2 36.7 1.0 CB E:ASP74 4.3 29.0 1.0 CG E:GLU78 4.3 31.4 1.0 O E:HOH2028 4.3 32.0 1.0 OD1 G:ASP63 4.5 37.8 1.0 NE1 G:TRP48 4.7 27.3 1.0 CG G:ASP63 4.8 33.3 1.0 NE2 G:HIS44 4.9 31.3 1.0 CD1 G:TRP48 4.9 29.8 1.0 CD2 G:HIS59 4.9 29.3 1.0

Zinc binding site 10 out of 24 in the Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Identification of Two Zinc-Binding Sites in the Streptococcus Suis Dpr Protein within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1174 b:48.7 occ:1.00 ND1 E:HIS44 2.0 30.0 1.0 NE2 E:HIS40 2.2 38.3 1.0 O E:HOH2083 2.5 54.2 1.0 CE1 E:HIS44 2.8 32.4 1.0 CD2 E:HIS40 3.0 35.9 1.0 CG E:HIS44 3.1 28.8 1.0 CE1 E:HIS40 3.2 38.6 1.0 CB E:HIS44 3.6 30.9 1.0 O G:HOH2010 3.9 40.8 1.0 NE2 E:HIS44 4.0 30.6 1.0 CD2 E:HIS44 4.1 30.8 1.0 CG E:HIS40 4.2 33.8 1.0 ND1 E:HIS40 4.3 37.1 1.0 SD E:MET66 4.4 33.0 1.0 CD2 G:LEU73 4.5 34.6 1.0 O G:HOH2031 4.5 40.4 1.0 O E:HIS40 4.9 31.3 1.0 CA E:HIS44 5.0 30.4 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