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Zinc in PDB 5slq: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829, PDB code: 5slq was solved by N.Imprachim, Y.Yosaatmadja, F.Von-Delft, C.Bountra, O.Gileadi, J.A.Newman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.90 / 2.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.795, 68.648, 138.407, 90, 90, 90
R / Rfree (%) 23.6 / 27.4

Other elements in 5slq:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829 (pdb code 5slq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829, PDB code: 5slq:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slq

Go back to Zinc Binding Sites List in 5slq
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:42.0
occ:1.00
 ND1 D:HIS264 2.0 52.0 1.0
NE2 D:HIS257 2.1 46.7 1.0
SG D:CYS279 2.2 39.8 1.0
SG D:CYS261 2.3 46.5 1.0
CE1 D:HIS264 3.0 52.7 1.0
CD2 D:HIS257 3.0 45.8 1.0
CB D:CYS261 3.0 46.8 1.0
CG D:HIS264 3.1 50.9 1.0
CE1 D:HIS257 3.1 46.7 1.0
CB D:CYS279 3.3 37.6 1.0
CB D:HIS264 3.5 51.5 1.0
CG D:HIS257 4.1 45.3 1.0
NE2 D:HIS264 4.2 52.7 1.0
ND1 D:HIS257 4.2 46.8 1.0
CD2 D:HIS264 4.2 51.8 1.0
N D:HIS264 4.2 51.6 1.0
CA D:HIS264 4.5 52.4 1.0
CA D:CYS261 4.5 47.5 1.0
N D:ASP415 4.5 38.8 1.0
CA D:CYS279 4.7 37.3 1.0
CA D:CYS414 4.8 37.7 0.4
C D:CYS261 4.9 48.1 1.0
CA D:CYS414 4.9 38.8 0.6
SG D:CYS414 4.9 44.2 0.6
O D:HOH734 4.9 53.3 1.0

Zinc binding site 2 out of 3 in 5slq

Go back to Zinc Binding Sites List in 5slq
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:47.8
occ:1.00
 SG D:CYS484 2.2 45.7 1.0
ND1 D:HIS487 2.2 45.2 1.0
SG D:CYS452 2.2 52.1 1.0
SG D:CYS477 2.4 48.3 1.0
CE1 D:HIS487 3.1 45.2 1.0
CB D:CYS477 3.2 43.4 1.0
CB D:CYS452 3.3 56.1 1.0
CG D:HIS487 3.3 43.3 1.0
CB D:CYS484 3.3 45.1 1.0
CB D:HIS487 3.6 42.3 1.0
CA D:CYS452 3.9 57.6 1.0
N D:CYS484 4.0 45.6 1.0
CA D:CYS484 4.2 45.2 1.0
NE2 D:HIS487 4.3 45.1 1.0
CA D:CYS477 4.4 42.2 1.0
N D:CYS477 4.4 42.2 1.0
CD2 D:HIS487 4.4 44.2 1.0
N D:HIS487 4.5 42.2 1.0
N D:CYS452 4.6 56.0 1.0
CA D:HIS487 4.7 42.4 1.0
CB D:THR475 4.7 39.9 1.0
OG1 D:THR475 4.8 40.4 1.0
O D:CYS484 4.8 45.6 1.0
C D:CYS484 4.9 45.3 1.0
O D:HOH799 4.9 39.4 1.0

Zinc binding site 3 out of 3 in 5slq

Go back to Zinc Binding Sites List in 5slq
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434829 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:53.4
occ:1.00
 ND1 D:HIS229 1.9 51.0 1.0
SG D:CYS207 2.3 58.8 1.0
SG D:CYS210 2.4 57.3 1.0
SG D:CYS226 2.4 54.2 1.0
CE1 D:HIS229 2.7 51.5 1.0
CB D:CYS207 3.1 56.7 1.0
CG D:HIS229 3.2 48.9 1.0
CB D:CYS226 3.5 46.9 1.0
CB D:CYS210 3.5 54.9 1.0
CB D:HIS229 3.7 45.9 1.0
N D:CYS210 3.9 54.7 1.0
N D:CYS226 3.9 45.9 1.0
NE2 D:HIS229 4.0 51.5 1.0
CD2 D:HIS229 4.2 50.2 1.0
CA D:CYS210 4.2 54.6 1.0
CA D:CYS226 4.3 45.1 1.0
C D:LEU209 4.4 55.2 1.0
N D:HIS229 4.4 44.6 1.0
CA D:CYS207 4.5 56.3 1.0
NH1 D:ARG212 4.6 56.4 1.0
CB D:LEU209 4.6 56.5 1.0
CB D:ARG212 4.7 49.8 1.0
CA D:HIS229 4.7 45.0 1.0
C D:CYS210 4.7 54.5 1.0
N D:LEU209 4.8 56.1 1.0
CA D:LEU209 4.8 55.9 1.0
CD D:ARG212 4.8 52.2 1.0
CB D:HIS228 4.9 43.6 1.0
O D:CYS210 4.9 54.6 1.0
C D:CYS226 4.9 43.2 1.0
O D:LEU209 5.0 55.1 1.0

Reference:

N.Imprachim, Y.Yosaatmadja, F.Von-Delft, C.Bountra, O.Gileadi, J.A.Newman. Pandda Analysis Group Deposition To Be Published.
Page generated: Mon Oct 28 07:54:02 2024

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