Zinc in PDB 2xgw: Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr

The structure of Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr, PDB code: 2xgw was solved by T.Haikarainen, C.-C.Tsou, J.-J.Wu, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	107.83 / 2.10
Space group	F 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	187.120, 187.120, 187.120, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 17.2

The structure of Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr (pdb code 2xgw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr, PDB code: 2xgw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1176 b:12.0 occ:0.60 ZN A:ZN1176 0.0 12.0 0.6 ZN A:ZN1176 1.2 12.3 0.4 OD2 A:ASP77 2.0 17.9 1.0 O A:HOH2182 2.0 15.7 1.0 CG A:ASP77 2.9 13.5 1.0 OD1 A:ASP77 3.1 16.8 1.0 ZN A:ZN1177 3.5 19.3 1.0 OE2 A:GLU81 3.6 19.4 1.0 O A:HOH2187 3.8 21.0 1.0 O A:HOH2002 4.0 32.7 1.0 O A:HOH2185 4.2 36.5 1.0 CB A:ASP77 4.2 11.0 1.0 CD A:GLU81 4.3 15.5 1.0 OE1 A:GLU81 4.6 16.3 1.0 O A:HOH2082 4.9 24.4 1.0 O2 A:SIN1180 5.0 21.8 1.0

Zinc binding site 2 out of 4 in the Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1176 b:12.3 occ:0.40 ZN A:ZN1176 0.0 12.3 0.4 ZN A:ZN1176 1.2 12.0 0.6 O A:HOH2182 1.8 15.7 1.0 OD2 A:ASP77 1.9 17.9 1.0 OE2 A:GLU81 2.4 19.4 1.0 CG A:ASP77 2.7 13.5 1.0 ZN A:ZN1177 2.7 19.3 1.0 OD1 A:ASP77 2.8 16.8 1.0 CD A:GLU81 3.1 15.5 1.0 OE1 A:GLU81 3.5 16.3 1.0 O A:HOH2185 4.0 36.5 1.0 CG A:GLU81 4.1 13.2 1.0 CB A:ASP77 4.2 11.0 1.0 O A:HOH2187 4.2 21.0 1.0 O2 A:SIN1180 4.3 21.8 1.0 O A:HOH2082 4.4 24.4 1.0 O A:HOH2002 4.5 32.7 1.0 O1 A:SIN1180 5.0 20.9 1.0

Zinc binding site 3 out of 4 in the Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1177 b:19.3 occ:1.00 O2 A:SIN1180 1.9 21.8 1.0 O A:HOH2182 1.9 15.7 1.0 OE2 A:GLU81 2.2 19.4 1.0 ZN A:ZN1176 2.7 12.3 0.4 C1 A:SIN1180 2.7 24.2 1.0 OE1 A:GLU81 2.8 16.3 1.0 O1 A:SIN1180 2.8 20.9 1.0 CD A:GLU81 2.9 15.5 1.0 ZN A:ZN1176 3.5 12.0 0.6 O A:HOH2187 3.6 21.0 1.0 O A:HOH2185 3.8 36.5 1.0 C2 A:SIN1180 4.2 28.7 1.0 OD2 A:ASP77 4.3 17.9 1.0 CG A:GLU81 4.3 13.2 1.0

Zinc binding site 4 out of 4 in the Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc-Bound Crystal Structure of Streptococcus Pyogenes Dpr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1178 b:35.7 occ:1.00 NE2 A:HIS100 2.0 22.7 1.0 O A:HOH2184 2.2 32.7 1.0 CL A:CL1179 2.3 45.8 1.0 O A:HOH2183 2.4 40.5 1.0 CD2 A:HIS100 3.0 18.0 1.0 CE1 A:HIS100 3.1 22.0 1.0 NZ A:LYS99 3.6 36.8 1.0 CD A:LYS99 4.0 30.3 1.0 CG A:HIS100 4.1 19.2 1.0 ND1 A:HIS100 4.2 19.4 1.0 CG A:GLU96 4.3 17.4 1.0 OE2 A:GLU96 4.4 24.6 1.0 CE A:LYS99 4.4 33.8 1.0 CE1 A:TYR91 4.5 14.6 1.0 O A:HOH2025 4.6 50.2 1.0 CB A:GLU96 4.8 15.0 1.0 CD A:GLU96 4.9 20.7 1.0 CA A:GLU96 4.9 14.1 1.0 CG A:LYS99 5.0 22.9 1.0

T.Haikarainen, C.-C.Tsou, J.-J.Wu, A.C.Papageorgiou. Structural Characterization and Biological Implications of Di-Zinc Binding in the Ferroxidase Center of Streptococcus Pyogenes Dpr. Biochem.Biophys.Res.Commun. V. 398 361 2010.
ISSN: ISSN 0006-291X
PubMed: 20599728
DOI: 10.1016/J.BBRC.2010.06.071