Zinc in PDB 6r5e: Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp, PDB code: 6r5e 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)	46.41 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.500, 117.180, 152.090, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.6

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Manganese	(Mn)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp (pdb code 6r5e). 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 PRI1 Subunit of Human Primase Bound to 2F-Atp, PDB code: 6r5e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp


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 Bound to 2F-Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:38.3 occ:1.00 SG A:CYS121 2.3 39.0 1.0 SG A:CYS122 2.4 42.8 1.0 SG A:CYS131 2.4 34.1 1.0 SG A:CYS128 2.4 40.2 1.0 HB2 A:CYS121 3.0 48.8 1.0 HB3 A:CYS131 3.1 43.6 1.0 HB2 A:CYS122 3.1 50.8 1.0 HB3 A:CYS128 3.2 48.8 1.0 H A:CYS128 3.2 42.0 1.0 CB A:CYS121 3.3 40.6 1.0 CB A:CYS128 3.3 40.7 1.0 CB A:CYS131 3.3 36.4 1.0 CB A:CYS122 3.3 42.3 1.0 H A:CYS131 3.3 46.5 1.0 N A:CYS128 3.5 35.0 1.0 N A:CYS122 3.8 39.5 1.0 N A:CYS131 3.8 38.7 1.0 H A:CYS122 3.8 47.4 1.0 CA A:CYS128 3.9 37.4 1.0 HB2 A:LYS130 3.9 53.1 1.0 HB3 A:CYS121 4.0 48.8 1.0 HH11 A:ARG119 4.0 45.3 1.0 HA A:ILE127 4.0 42.1 1.0 C A:CYS121 4.0 43.9 1.0 HB2 A:CYS131 4.1 43.6 1.0 HB3 A:CYS122 4.1 50.8 1.0 O A:CYS128 4.1 39.2 1.0 CA A:CYS122 4.1 39.8 1.0 HD2 A:ARG119 4.2 57.1 1.0 HB2 A:CYS128 4.2 48.8 1.0 CA A:CYS131 4.2 35.7 1.0 CA A:CYS121 4.2 42.8 1.0 C A:ILE127 4.2 34.9 1.0 C A:CYS128 4.2 38.8 1.0 H A:LYS130 4.2 46.5 1.0 HZ3 E:LYS176 4.3 70.9 1.0 HE22 A:GLN231 4.4 51.0 1.0 H A:CYS121 4.5 47.2 1.0 NH1 A:ARG119 4.5 37.7 1.0 C A:LYS130 4.6 41.5 1.0 O A:CYS121 4.6 46.7 1.0 CA A:ILE127 4.6 35.1 1.0 HA A:CYS122 4.6 47.8 1.0 HH12 A:ARG119 4.7 45.3 1.0 N A:LYS130 4.8 38.8 1.0 HA A:CYS128 4.8 44.9 1.0 CB A:LYS130 4.8 44.3 1.0 HA A:CYS131 4.8 42.8 1.0 N A:CYS121 4.8 39.3 1.0 CA A:LYS130 4.9 41.0 1.0 O A:ILE127 5.0 36.1 1.0 HA A:CYS121 5.0 51.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to 2F-Atp


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 PRI1 Subunit of Human Primase Bound to 2F-Atp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn501 b:37.8 occ:1.00 SG E:CYS121 2.3 42.5 1.0 SG E:CYS122 2.3 45.9 1.0 SG E:CYS131 2.4 35.6 1.0 SG E:CYS128 2.4 40.7 1.0 HB2 E:CYS121 3.0 55.4 1.0 HB2 E:CYS122 3.0 56.7 1.0 HB3 E:CYS131 3.1 44.6 1.0 H E:CYS128 3.2 46.5 1.0 CB E:CYS121 3.2 46.2 1.0 CB E:CYS122 3.3 47.2 1.0 HB3 E:CYS128 3.3 48.6 1.0 CB E:CYS131 3.3 37.2 1.0 CB E:CYS128 3.4 40.5 1.0 H E:CYS131 3.4 51.6 1.0 N E:CYS128 3.5 38.8 1.0 N E:CYS122 3.8 46.5 1.0 HH11 E:ARG119 3.8 51.6 1.0 HB2 E:LYS130 3.8 65.9 1.0 N E:CYS131 3.8 43.0 1.0 H E:CYS122 3.9 55.8 1.0 CA E:CYS128 3.9 38.9 1.0 C E:CYS121 3.9 48.8 1.0 HA E:ILE127 3.9 50.0 1.0 HD2 E:ARG119 3.9 54.1 1.0 HB3 E:CYS121 3.9 55.4 1.0 HB3 E:CYS122 4.0 56.7 1.0 HB2 E:CYS131 4.1 44.6 1.0 CA E:CYS122 4.1 48.0 1.0 O E:CYS128 4.1 41.0 1.0 CA E:CYS121 4.1 47.6 1.0 C E:ILE127 4.2 41.5 1.0 H E:LYS130 4.2 52.4 1.0 CA E:CYS131 4.2 40.2 1.0 HB2 E:CYS128 4.2 48.6 1.0 C E:CYS128 4.3 40.9 1.0 NH1 E:ARG119 4.3 43.0 1.0 HE22 E:GLN231 4.4 55.0 1.0 O E:CYS121 4.4 53.2 1.0 H E:CYS121 4.5 54.5 1.0 HH12 E:ARG119 4.5 51.6 1.0 C E:LYS130 4.5 47.8 1.0 CA E:ILE127 4.6 41.7 1.0 CB E:LYS130 4.6 54.9 1.0 HA E:CYS122 4.6 57.6 1.0 N E:LYS130 4.7 43.6 1.0 HA E:CYS128 4.8 46.7 1.0 HB3 E:LYS130 4.8 65.9 1.0 N E:CYS121 4.8 45.4 1.0 CA E:LYS130 4.8 47.7 1.0 HA E:CYS131 4.9 48.3 1.0 CD E:ARG119 4.9 45.1 1.0 O E:ILE127 4.9 41.6 1.0 HA E:CYS121 4.9 57.1 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