Zinc in PDB 6rb4: Crystal Structure of the PRI1 Subunit of Human Primase

The structure of Crystal Structure of the PRI1 Subunit of Human Primase, PDB code: 6rb4 was solved by M.L.Kilkenny, L.Pellegrini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.50 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.659, 78.659, 148.335, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.5

The binding sites of Zinc atom in the Crystal Structure of the PRI1 Subunit of Human Primase (pdb code 6rb4). 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 PRI1 Subunit of Human Primase, PDB code: 6rb4:

Zinc binding site 1 out of 1 in the Crystal Structure of the PRI1 Subunit of Human 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 PRI1 Subunit of Human Primase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:19.2 occ:1.00 SG A:CYS131 2.3 17.5 1.0 SG A:CYS122 2.3 19.7 1.0 SG A:CYS121 2.3 21.3 1.0 SG A:CYS128 2.4 20.6 1.0 H A:CYS131 3.0 23.5 1.0 HB2 A:CYS121 3.0 24.4 1.0 HB2 A:CYS122 3.1 23.8 1.0 HB3 A:CYS131 3.2 19.9 1.0 HB3 A:CYS128 3.2 20.8 1.0 H A:CYS128 3.2 23.8 1.0 CB A:CYS121 3.3 20.5 1.0 CB A:CYS122 3.3 20.0 1.0 CB A:CYS128 3.3 17.4 1.0 CB A:CYS131 3.3 16.8 1.0 N A:CYS128 3.5 20.0 1.0 HH11 A:ARG119 3.5 24.6 1.0 HB2 A:LYS130 3.7 32.0 1.0 HA A:ILE127 3.7 25.2 1.0 N A:CYS131 3.7 19.7 1.0 H A:CYS122 3.8 26.6 1.0 N A:CYS122 3.8 22.3 1.0 HD2 A:ARG119 3.9 26.4 1.0 CA A:CYS128 3.9 21.4 1.0 HB3 A:CYS121 3.9 24.4 1.0 C A:ILE127 4.1 19.8 1.0 HB3 A:CYS122 4.1 23.8 1.0 C A:CYS121 4.1 26.5 1.0 HB2 A:CYS131 4.1 19.9 1.0 CA A:CYS131 4.1 17.7 1.0 CA A:CYS122 4.1 21.6 1.0 NH1 A:ARG119 4.2 20.6 1.0 HB2 A:CYS128 4.2 20.8 1.0 CA A:CYS121 4.3 22.3 1.0 HH12 A:ARG119 4.3 24.6 1.0 O A:CYS128 4.4 17.2 1.0 HE22 A:GLN231 4.4 34.1 1.0 C A:CYS128 4.4 19.7 1.0 CA A:ILE127 4.4 21.1 1.0 H A:LYS130 4.5 22.0 1.0 HA A:CYS122 4.5 25.8 1.0 H A:CYS121 4.6 27.2 1.0 CB A:LYS130 4.6 26.8 1.0 HA3 A:GLY-2 4.7 28.0 1.0 HA A:CYS131 4.7 21.1 1.0 HA A:CYS128 4.8 25.6 1.0 O A:CYS121 4.8 23.4 1.0 CD A:ARG119 4.8 22.1 1.0 C A:LYS130 4.8 25.6 1.0 O A:ILE127 4.9 20.0 1.0 HB3 A:ARG119 4.9 29.7 1.0 HD2 A:LYS130 5.0 42.3 1.0 N A:CYS121 5.0 22.8 1.0 N A:LYS130 5.0 18.4 1.0 HB3 A:LYS130 5.0 32.0 1.0

S.Holzer, N.J.Rzechorzek, I.R.Short, M.Jenkyn-Bedford, L.Pellegrini, M.L.Kilkenny. Structural Basis For Inhibition of Human Primase By Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine. Acs Chem.Biol. V. 14 1904 2019.
ISSN: ESSN 1554-8937
PubMed: 31479243
DOI: 10.1021/ACSCHEMBIO.9B00367