Zinc in PDB 6r4t: Crystal Structure of the PRI1 Subunit of Human Primase Bound to Vidarabine Triphosphate

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to Vidarabine Triphosphate, PDB code: 6r4t 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)	46.69 / 2.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	111.090, 118.970, 150.720, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 23.9

The structure of Crystal Structure of the PRI1 Subunit of Human Primase Bound to Vidarabine Triphosphate also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to Vidarabine Triphosphate (pdb code 6r4t). 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 Vidarabine Triphosphate, PDB code: 6r4t:
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 Vidarabine Triphosphate


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 Vidarabine Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:68.9 occ:1.00 SG A:CYS128 2.2 77.5 1.0 SG A:CYS122 2.2 76.8 1.0 SG A:CYS121 2.2 72.3 1.0 SG A:CYS131 2.5 63.3 1.0 HB2 A:CYS121 3.0 90.0 1.0 HB3 A:CYS131 3.1 76.2 1.0 HB2 A:CYS122 3.2 93.0 1.0 CB A:CYS121 3.2 75.0 1.0 HB3 A:CYS128 3.3 92.7 1.0 CB A:CYS122 3.3 77.5 1.0 CB A:CYS128 3.3 77.3 1.0 H A:CYS131 3.3 82.2 1.0 CB A:CYS131 3.4 63.5 1.0 H A:CYS128 3.5 90.1 1.0 H A:CYS122 3.5 95.5 1.0 N A:CYS122 3.6 79.6 1.0 N A:CYS128 3.7 75.1 1.0 HB2 A:LYS130 3.8 0.8 1.0 C A:CYS121 3.8 77.5 1.0 HD2 A:ARG119 3.8 91.1 1.0 N A:CYS131 3.9 68.6 1.0 HB3 A:CYS121 4.0 90.0 1.0 CA A:CYS128 4.0 75.7 1.0 CA A:CYS122 4.0 80.1 1.0 HB3 A:CYS122 4.1 93.0 1.0 HA A:ILE127 4.1 85.1 1.0 HH11 A:ARG119 4.1 79.5 1.0 HB2 A:CYS128 4.1 92.7 1.0 CA A:CYS121 4.1 79.0 1.0 HB2 A:CYS131 4.2 76.2 1.0 O A:CYS128 4.2 78.0 1.0 CA A:CYS131 4.3 64.3 1.0 C A:ILE127 4.3 68.5 1.0 H A:LYS130 4.3 96.4 1.0 C A:CYS128 4.4 76.6 1.0 O A:CYS121 4.4 76.4 1.0 HA A:CYS122 4.5 96.1 1.0 HE22 A:GLN231 4.5 86.6 1.0 H A:CYS121 4.5 99.6 1.0 CB A:LYS130 4.6 94.0 1.0 HB3 A:LYS130 4.7 0.8 1.0 CD A:ARG119 4.7 76.0 1.0 CA A:ILE127 4.7 70.9 1.0 C A:LYS130 4.8 80.3 1.0 HD3 A:ARG119 4.8 91.1 1.0 N A:LYS130 4.8 80.4 1.0 NH1 A:ARG119 4.8 66.3 1.0 N A:CYS121 4.9 83.0 1.0 HA A:CYS128 4.9 90.8 1.0 HA A:CYS121 4.9 94.8 1.0 HA A:CYS131 4.9 77.2 1.0 CA A:LYS130 5.0 85.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the PRI1 Subunit of Human Primase Bound to Vidarabine Triphosphate


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 Vidarabine Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:71.3 occ:1.00 SG D:CYS122 2.2 78.9 1.0 SG D:CYS121 2.3 68.8 1.0 SG D:CYS128 2.3 69.7 1.0 SG D:CYS131 2.4 62.3 1.0 HB3 D:CYS131 2.9 73.8 1.0 HB2 D:CYS122 3.0 96.5 1.0 HB2 D:CYS121 3.1 86.3 1.0 CB D:CYS122 3.2 80.5 1.0 CB D:CYS131 3.3 61.5 1.0 CB D:CYS121 3.3 71.9 1.0 H D:CYS131 3.3 82.0 1.0 H D:CYS128 3.4 90.8 1.0 HB3 D:CYS128 3.4 86.0 1.0 CB D:CYS128 3.4 71.7 1.0 H D:CYS122 3.5 0.8 1.0 N D:CYS122 3.5 84.8 1.0 N D:CYS128 3.6 75.7 1.0 HD2 D:ARG119 3.8 89.1 1.0 HB2 D:LYS130 3.8 0.0 1.0 N D:CYS131 3.8 68.3 1.0 HH11 D:ARG119 3.9 82.1 1.0 C D:CYS121 3.9 75.6 1.0 HA D:ILE127 4.0 91.0 1.0 CA D:CYS122 4.0 84.0 1.0 HB2 D:CYS131 4.0 73.8 1.0 CA D:CYS128 4.0 74.4 1.0 HB3 D:CYS122 4.0 96.5 1.0 HB3 D:CYS121 4.1 86.3 1.0 CA D:CYS131 4.2 62.3 1.0 CA D:CYS121 4.2 75.0 1.0 O D:CYS128 4.2 77.0 1.0 HB2 D:CYS128 4.3 86.0 1.0 C D:ILE127 4.3 72.3 1.0 C D:CYS128 4.4 75.4 1.0 HE22 D:GLN231 4.4 89.7 1.0 H D:LYS130 4.4 0.9 1.0 O D:CYS121 4.5 78.7 1.0 HA D:CYS122 4.5 0.7 1.0 NH1 D:ARG119 4.5 68.4 1.0 H D:CYS121 4.5 93.6 1.0 CA D:ILE127 4.6 75.9 1.0 CB D:LYS130 4.6 95.9 1.0 C D:LYS130 4.7 85.4 1.0 CD D:ARG119 4.7 74.3 1.0 HB3 D:LYS130 4.8 0.0 1.0 HH12 D:ARG119 4.8 82.1 1.0 HA D:CYS131 4.8 74.8 1.0 HD3 D:ARG119 4.9 89.1 1.0 N D:LYS130 4.9 85.8 1.0 N D:CYS121 4.9 78.0 1.0 HA D:CYS128 4.9 89.2 1.0 HA D:CYS121 5.0 90.0 1.0 CA D:LYS130 5.0 89.5 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