Zinc in PDB 5of3: Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus.

The structure of Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus., PDB code: 5of3 was solved by L.Pellegrini, S.Holzer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.91 / 2.91
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	104.889, 104.889, 229.758, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 27.1

The structure of Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus. also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus. (pdb code 5of3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus., PDB code: 5of3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:91.9 occ:1.00 OD2 A:ASP131 2.0 97.2 1.0 SG A:CYS119 2.3 91.8 1.0 SG A:CYS128 2.3 81.3 1.0 SG A:CYS116 2.3 86.1 1.0 CG A:ASP131 3.1 97.1 1.0 CB A:CYS119 3.1 74.8 1.0 CB A:CYS116 3.1 74.2 1.0 CB A:CYS128 3.4 70.2 1.0 N A:CYS119 3.7 86.8 1.0 OD1 A:ASP131 3.9 89.0 1.0 CB A:ASP131 3.9 98.9 1.0 CA A:CYS119 4.0 85.0 1.0 N A:ASP131 4.5 0.6 1.0 CA A:CYS116 4.6 71.7 1.0 CB A:VAL118 4.7 81.5 1.0 C A:VAL118 4.7 82.5 1.0 CB A:ARG130 4.8 84.2 1.0 CA A:CYS128 4.9 76.1 1.0 C A:CYS119 4.9 75.7 1.0 CA A:ASP131 4.9 0.5 1.0 N A:GLY120 5.0 79.0 1.0 C A:CYS116 5.0 87.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Heterotrimeric Prislx Primase From S. Solfataricus. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1003 b:0.3 occ:1.00 OD2 D:ASP131 2.0 0.4 1.0 SG D:CYS128 2.3 1.0 1.0 SG D:CYS119 2.3 0.9 1.0 SG D:CYS116 2.3 0.6 1.0 CG D:ASP131 3.0 0.6 1.0 CB D:CYS116 3.0 0.9 1.0 CB D:CYS128 3.2 0.2 1.0 CB D:CYS119 3.3 0.7 1.0 CB D:ASP131 3.7 0.7 1.0 N D:CYS119 3.8 0.7 1.0 OD1 D:ASP131 3.8 0.5 1.0 N D:ASP131 4.1 0.6 1.0 CA D:CYS119 4.1 0.3 1.0 CA D:CYS116 4.5 0.1 1.0 CA D:ASP131 4.5 0.1 1.0 CA D:CYS128 4.6 0.8 1.0 CB D:ARG130 4.7 0.2 1.0 CB D:VAL118 4.8 0.6 1.0 C D:VAL118 4.8 0.5 1.0 C D:CYS116 4.9 0.1 1.0 C D:CYS119 4.9 0.1 1.0 O D:CYS116 5.0 0.6 1.0

S.Holzer, J.Yan, M.L.Kilkenny, S.D.Bell, L.Pellegrini. Primer Synthesis By A Eukaryotic-Like Archaeal Primase Is Independent of Its Fe-S Cluster. Nat Commun V. 8 1718 2017.
ISSN: ESSN 2041-1723
PubMed: 29167441
DOI: 10.1038/S41467-017-01707-W