Zinc in PDB 1d0q: Structure of the Zinc-Binding Domain of Bacillus Stearothermophilus Dna Primase

The structure of Structure of the Zinc-Binding Domain of Bacillus Stearothermophilus Dna Primase, PDB code: 1d0q was solved by H.Pan, D.B.Wigley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.170, 58.745, 45.750, 90.00, 91.73, 90.00
R / Rfree (%)	20.4 / 22.5

The binding sites of Zinc atom in the Structure of the Zinc-Binding Domain of Bacillus Stearothermophilus Dna Primase (pdb code 1d0q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Zinc-Binding Domain of Bacillus Stearothermophilus Dna Primase, PDB code: 1d0q:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Zinc-Binding Domain of Bacillus Stearothermophilus Dna Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Zinc-Binding Domain of Bacillus Stearothermophilus Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn151 b:15.0 occ:1.00 ND1 A:HIS43 2.3 16.0 1.0 SG A:CYS40 2.4 14.3 1.0 SG A:CYS64 2.4 19.2 1.0 SG A:CYS61 2.5 18.5 1.0 CE1 A:HIS43 2.9 17.3 1.0 CB A:CYS40 3.0 14.2 1.0 CB A:CYS61 3.2 21.3 1.0 CG A:HIS43 3.3 22.2 1.0 CB A:CYS64 3.3 21.5 1.0 CB A:HIS43 3.5 20.1 1.0 N A:CYS64 3.8 20.5 1.0 N A:HIS43 3.9 21.5 1.0 CA A:CYS64 4.0 20.2 1.0 NE2 A:HIS43 4.1 15.2 1.0 CD2 A:HIS43 4.2 16.0 1.0 CA A:HIS43 4.2 18.7 1.0 C A:GLY63 4.2 18.6 1.0 CB A:PHE42 4.3 13.3 1.0 CA A:CYS40 4.5 18.2 1.0 OG A:SER49 4.6 19.0 1.0 C A:PHE42 4.7 21.2 1.0 CA A:CYS61 4.7 19.6 1.0 O A:HIS43 4.8 19.4 1.0 O A:GLY63 4.8 22.1 1.0 C A:CYS64 4.8 25.9 1.0 CA A:GLY63 4.9 21.9 1.0 C A:HIS43 4.9 19.3 1.0 N A:GLY63 4.9 22.3 1.0 CA A:PHE42 4.9 15.0 1.0 N A:PHE42 5.0 14.5 1.0

Zinc binding site 2 out of 2 in the Structure of the Zinc-Binding Domain of Bacillus Stearothermophilus Dna Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Zinc-Binding Domain of Bacillus Stearothermophilus Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn151 b:15.0 occ:1.00 ND1 B:HIS43 2.3 18.9 1.0 SG B:CYS61 2.3 17.3 1.0 SG B:CYS40 2.3 15.4 1.0 SG B:CYS64 2.4 20.1 1.0 CB B:CYS40 3.0 17.7 1.0 CE1 B:HIS43 3.0 16.8 1.0 CB B:CYS61 3.1 17.9 1.0 CB B:CYS64 3.2 23.1 1.0 CG B:HIS43 3.3 20.8 1.0 CB B:HIS43 3.7 20.7 1.0 N B:CYS64 3.7 24.2 1.0 CA B:CYS64 4.0 25.7 1.0 N B:HIS43 4.0 20.6 1.0 NE2 B:HIS43 4.2 18.4 1.0 CD2 B:HIS43 4.4 20.8 1.0 CA B:HIS43 4.4 20.3 1.0 CA B:CYS40 4.5 18.2 1.0 C B:GLY63 4.5 24.4 1.0 CA B:CYS61 4.5 19.4 1.0 CB B:PHE42 4.6 15.3 1.0 CB B:ALA66 4.6 19.5 1.0 OG B:SER49 4.6 18.3 1.0 C B:PHE42 4.7 23.4 1.0 C B:CYS64 4.8 27.5 1.0 O B:HIS43 4.8 19.7 1.0 CA B:GLY63 4.9 23.7 1.0 N B:GLY63 4.9 22.6 1.0 N B:GLY65 4.9 27.9 1.0 C B:HIS43 5.0 19.7 1.0

H.Pan, D.B.Wigley. Structure of the Zinc-Binding Domain of Bacillus Stearothermophilus Dna Primase. Structure Fold.Des. V. 8 231 2000.
ISSN: ISSN 0969-2126
PubMed: 10745010
DOI: 10.1016/S0969-2126(00)00101-5