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Zinc in PDB 5sky: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z466628048

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z466628048, PDB code: 5sky 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) 60.90 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.85, 68.59, 138.13, 90, 90, 90
R / Rfree (%) 21.3 / 24.8

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 Z466628048 (pdb code 5sky). 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 Z466628048, PDB code: 5sky:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sky

Go back to Zinc Binding Sites List in 5sky
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z466628048


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 Z466628048 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:38.7
occ:1.00
 ND1 D:HIS264 2.0 43.1 1.0
NE2 D:HIS257 2.2 43.1 1.0
SG D:CYS279 2.3 36.4 1.0
SG D:CYS261 2.4 42.8 1.0
CE1 D:HIS264 2.8 43.4 1.0
CD2 D:HIS257 3.0 42.5 1.0
CB D:CYS261 3.1 43.1 1.0
CB D:CYS279 3.1 36.2 1.0
CG D:HIS264 3.2 42.7 1.0
CE1 D:HIS257 3.2 43.2 1.0
CB D:HIS264 3.7 45.5 1.0
NE2 D:HIS264 4.0 43.1 1.0
CG D:HIS257 4.2 42.0 1.0
CD2 D:HIS264 4.2 42.4 1.0
ND1 D:HIS257 4.3 42.9 1.0
N D:HIS264 4.4 47.1 1.0
CA D:CYS261 4.5 44.4 1.0
CA D:CYS279 4.6 36.0 1.0
N D:ASP415 4.6 36.9 1.0
CA D:HIS264 4.7 47.6 1.0
O D:HOH796 4.9 42.8 1.0
SG D:CYS414 4.9 44.2 0.6
CA D:CYS414 4.9 36.8 0.4
C D:CYS261 4.9 45.1 1.0
CA D:CYS414 5.0 37.4 0.6

Zinc binding site 2 out of 3 in 5sky

Go back to Zinc Binding Sites List in 5sky
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z466628048


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 Z466628048 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:43.5
occ:1.00
 ND1 D:HIS487 2.2 40.4 1.0
SG D:CYS484 2.3 39.5 1.0
SG D:CYS452 2.4 51.6 1.0
SG D:CYS477 2.4 42.7 1.0
CE1 D:HIS487 3.1 40.4 1.0
CB D:CYS452 3.2 52.5 1.0
CB D:CYS477 3.2 39.2 1.0
CG D:HIS487 3.2 39.1 1.0
CB D:CYS484 3.4 40.8 1.0
CB D:HIS487 3.6 38.3 1.0
CA D:CYS452 3.7 53.1 1.0
N D:CYS484 4.0 41.9 1.0
CA D:CYS484 4.3 41.4 1.0
NE2 D:HIS487 4.3 40.4 1.0
CD2 D:HIS487 4.4 39.4 1.0
N D:CYS477 4.4 39.7 1.0
CA D:CYS477 4.4 39.5 1.0
N D:CYS452 4.5 51.6 1.0
N D:HIS487 4.5 38.3 1.0
CA D:HIS487 4.7 38.7 1.0
CB D:THR475 4.7 38.1 1.0
OG1 D:THR475 4.7 38.3 1.0
O D:HOH831 4.9 40.1 1.0
C D:CYS484 5.0 41.9 1.0
O D:CYS484 5.0 42.7 1.0

Zinc binding site 3 out of 3 in 5sky

Go back to Zinc Binding Sites List in 5sky
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z466628048


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 Z466628048 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:49.0
occ:1.00
 ND1 D:HIS229 1.9 47.9 1.0
SG D:CYS207 2.2 50.0 1.0
SG D:CYS210 2.3 54.7 1.0
SG D:CYS226 2.5 46.6 1.0
CE1 D:HIS229 2.7 48.5 1.0
CB D:CYS207 3.0 49.9 1.0
CG D:HIS229 3.1 45.5 1.0
CB D:CYS210 3.3 51.4 1.0
CB D:CYS226 3.5 43.0 1.0
CB D:HIS229 3.7 41.9 1.0
N D:CYS210 3.7 50.6 1.0
NE2 D:HIS229 3.9 47.8 1.0
CA D:CYS210 4.0 50.5 1.0
N D:CYS226 4.0 42.2 1.0
CD2 D:HIS229 4.2 46.6 1.0
NH1 D:ARG212 4.2 44.6 1.0
C D:LEU209 4.3 51.5 1.0
CA D:CYS226 4.3 41.8 1.0
N D:HIS229 4.4 41.0 1.0
CA D:CYS207 4.5 50.0 1.0
C D:CYS210 4.5 50.4 1.0
CD D:ARG212 4.7 47.2 1.0
CA D:HIS229 4.7 41.1 1.0
CB D:LEU209 4.7 51.9 1.0
N D:LEU209 4.7 51.8 1.0
CB D:ARG212 4.8 46.5 1.0
CA D:LEU209 4.8 51.7 1.0
O D:CYS210 4.8 50.5 1.0
CB D:HIS228 4.9 40.5 1.0
O D:LEU209 5.0 52.0 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 07:42:27 2024

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