Zinc in PDB 4lim: Crystal Structure of the Catalytic Subunit of Yeast Primase

The structure of Crystal Structure of the Catalytic Subunit of Yeast Primase, PDB code: 4lim was solved by S.Vaithiyalingam, W.J.Chazin, J.M.Berger, J.Corn, S.Stephenson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 1.63
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.166, 43.624, 69.383, 83.11, 83.25, 78.00
R / Rfree (%)	15.5 / 18.9

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Subunit of Yeast Primase (pdb code 4lim). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Catalytic Subunit of Yeast Primase, PDB code: 4lim:

Zinc binding site 1 out of 1 in the Crystal Structure of the Catalytic Subunit of Yeast 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 Catalytic Subunit of Yeast Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.9 occ:1.00 SG A:CYS123 2.2 21.9 1.0 SG A:CYS124 2.3 22.9 1.0 SG A:CYS130 2.3 24.7 1.0 SG A:CYS133 2.3 17.8 1.0 CB A:CYS124 3.2 24.1 1.0 CB A:CYS123 3.3 32.3 1.0 CB A:CYS130 3.4 24.2 1.0 CB A:CYS133 3.5 17.3 1.0 N A:CYS130 3.5 18.4 1.0 N A:CYS133 3.6 18.2 1.0 N A:CYS124 3.7 25.4 1.0 C A:CYS123 3.9 27.6 1.0 CA A:CYS130 3.9 22.4 1.0 CA A:CYS124 4.0 26.2 1.0 C A:VAL129 4.1 19.6 1.0 CA A:CYS133 4.1 20.2 1.0 CA A:CYS123 4.3 27.9 1.0 O A:CYS130 4.3 21.4 1.0 O A:CYS123 4.3 26.7 1.0 C A:CYS130 4.4 21.6 1.0 CA A:VAL129 4.4 18.0 1.0 NH1 A:ARG121 4.5 25.9 1.0 CB A:LYS132 4.7 24.9 1.0 C A:LYS132 4.7 20.4 1.0 CD A:ARG121 4.9 18.4 1.0 N A:LYS132 4.9 23.3 1.0 O A:VAL129 4.9 22.0 1.0 N A:CYS123 5.0 26.2 1.0

S.Vaithiyalingam, D.R.Arnett, A.Aggarwal, B.F.Eichman, E.Fanning, W.J.Chazin. Insights Into Eukaryotic Primer Synthesis From Structures of the P48 Subunit of Human Dna Primase. J.Mol.Biol. V. 426 558 2014.
ISSN: ISSN 0022-2836
PubMed: 24239947
DOI: 10.1016/J.JMB.2013.11.007