Zinc in PDB 3lgb: Crystal Structure of the Fe-S Domain of the Yeast Dna Primase

The structure of Crystal Structure of the Fe-S Domain of the Yeast Dna Primase, PDB code: 3lgb was solved by L.Sauguet, L.Pellegrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.34 / 1.54
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	86.570, 86.570, 141.480, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 16.4

The structure of Crystal Structure of the Fe-S Domain of the Yeast Dna Primase also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase (pdb code 3lgb). 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 Fe-S Domain of the Yeast Dna Primase, PDB code: 3lgb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase


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 Fe-S Domain of the Yeast Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn515 b:22.9 occ:0.42 O B:HOH298 2.0 47.6 1.0 O B:HOH301 2.0 43.9 1.0 NE2 B:HIS348 2.0 27.5 1.0 O B:HOH299 2.1 50.8 1.0 O B:HOH300 2.2 42.8 1.0 O B:HOH171 2.2 42.2 1.0 CE1 B:HIS348 2.9 27.4 1.0 CD2 B:HIS348 3.2 25.6 1.0 O B:LYS345 3.7 21.4 1.0 O B:HOH603 3.8 45.2 1.0 ND1 B:HIS348 4.1 28.0 1.0 CG B:HIS348 4.2 23.6 1.0 O B:HOH571 4.8 52.7 1.0 O B:LYS346 4.8 23.4 1.0 C B:LYS345 4.9 21.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Fe-S Domain of the Yeast Dna Primase


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 Fe-S Domain of the Yeast Dna Primase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn516 b:14.5 occ:1.00 OE2 B:GLU389 1.9 17.3 1.0 CD B:GLU389 2.8 15.6 1.0 OE1 B:GLU389 2.9 17.2 1.0 O B:HOH599 4.0 26.4 1.0 O B:HOH570 4.0 31.9 1.0 O B:HOH162 4.1 29.7 1.0 CG B:GLU389 4.2 13.6 1.0

L.Sauguet, S.Klinge, R.L.Perera, J.D.Maman, L.Pellegrini. Shared Active Site Architecture Between the Large Subunit of Eukaryotic Primase and Dna Photolyase Plos One V. 5 10083 2010.
ISSN: ESSN 1932-6203
PubMed: 20404922
DOI: 10.1371/JOURNAL.PONE.0010083