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

Protein crystallography data

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

Other elements in 6r4t:

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

Zinc Binding Sites:

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 6r4t

Go back to Zinc Binding Sites List in 6r4t
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 6r4t

Go back to Zinc Binding Sites List in 6r4t
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

Reference:

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
Page generated: Wed Dec 16 12:35:47 2020

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