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Zinc in PDB 5sl5: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32014663

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32014663, PDB code: 5sl5 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) 48.86 / 2.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.28, 68.7, 138.99, 90, 90, 90
R / Rfree (%) 22.2 / 28.1

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 Z32014663 (pdb code 5sl5). 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 Z32014663, PDB code: 5sl5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sl5

Go back to Zinc Binding Sites List in 5sl5
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32014663


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 Z32014663 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:47.0
occ:1.00
 ND1 D:HIS264 1.9 59.3 1.0
NE2 D:HIS257 2.0 47.3 1.0
SG D:CYS261 2.3 51.6 1.0
SG D:CYS279 2.3 38.3 1.0
CE1 D:HIS264 2.8 59.7 1.0
CD2 D:HIS257 3.0 47.0 1.0
CB D:CYS261 3.0 51.5 1.0
CE1 D:HIS257 3.0 47.7 1.0
CG D:HIS264 3.1 57.8 1.0
CB D:CYS279 3.3 39.8 1.0
CB D:HIS264 3.5 57.3 1.0
NE2 D:HIS264 4.0 59.4 1.0
CG D:HIS257 4.1 46.8 1.0
ND1 D:HIS257 4.1 48.1 1.0
CD2 D:HIS264 4.1 58.5 1.0
N D:HIS264 4.2 57.2 1.0
CA D:CYS261 4.4 52.0 1.0
CA D:HIS264 4.5 58.0 1.0
N D:ASP415 4.7 42.8 1.0
CA D:CYS279 4.7 41.0 1.0
C D:CYS261 4.8 53.2 1.0
O D:CYS261 4.8 53.2 1.0
SG D:CYS414 4.9 45.9 0.6
O D:HIS264 5.0 61.3 1.0

Zinc binding site 2 out of 3 in 5sl5

Go back to Zinc Binding Sites List in 5sl5
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32014663


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 Z32014663 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:50.9
occ:1.00
 SG D:CYS484 2.2 46.2 1.0
ND1 D:HIS487 2.2 46.3 1.0
SG D:CYS452 2.3 64.3 1.0
SG D:CYS477 2.4 51.7 1.0
CE1 D:HIS487 3.0 46.1 1.0
CB D:CYS477 3.2 48.3 1.0
CB D:CYS452 3.2 63.1 1.0
CG D:HIS487 3.3 45.2 1.0
CB D:CYS484 3.3 49.5 1.0
CB D:HIS487 3.7 45.1 1.0
CA D:CYS452 3.7 63.6 1.0
N D:CYS484 4.0 51.5 1.0
NE2 D:HIS487 4.2 46.3 1.0
CA D:CYS484 4.2 50.5 1.0
CD2 D:HIS487 4.3 45.7 1.0
CA D:CYS477 4.4 48.2 1.0
N D:CYS477 4.4 48.5 1.0
N D:CYS452 4.5 61.8 1.0
N D:HIS487 4.5 45.9 1.0
CA D:HIS487 4.7 45.6 1.0
OG1 D:THR475 4.9 46.6 1.0
O D:HOH751 4.9 39.0 1.0
C D:CYS484 4.9 50.9 1.0
CB D:THR475 4.9 45.5 1.0
O D:CYS484 4.9 51.9 1.0

Zinc binding site 3 out of 3 in 5sl5

Go back to Zinc Binding Sites List in 5sl5
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z32014663


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 Z32014663 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:51.8
occ:1.00
 ND1 D:HIS229 1.9 49.5 1.0
SG D:CYS207 2.4 58.3 1.0
SG D:CYS226 2.4 50.4 1.0
SG D:CYS210 2.4 62.1 1.0
CE1 D:HIS229 2.6 50.0 1.0
CB D:CYS207 3.0 57.2 1.0
CG D:HIS229 3.2 48.4 1.0
CB D:CYS226 3.4 46.8 1.0
CB D:CYS210 3.4 57.9 1.0
N D:CYS210 3.8 57.5 1.0
CB D:HIS229 3.9 47.4 1.0
NE2 D:HIS229 3.9 50.0 1.0
N D:CYS226 3.9 46.5 1.0
CA D:CYS210 4.1 57.5 1.0
NH1 D:ARG212 4.1 59.4 1.0
CD2 D:HIS229 4.2 49.0 1.0
CA D:CYS226 4.3 45.8 1.0
CA D:CYS207 4.5 57.3 1.0
N D:HIS229 4.5 46.7 1.0
C D:LEU209 4.5 58.0 1.0
C D:CYS210 4.6 57.9 1.0
CB D:ARG212 4.6 54.0 1.0
CD D:ARG212 4.6 57.3 1.0
CB D:LEU209 4.8 58.1 1.0
CA D:HIS229 4.9 47.4 1.0
CG D:ARG212 4.9 55.8 1.0
O D:CYS210 5.0 58.3 1.0
CB D:HIS228 5.0 46.0 1.0
N D:LEU209 5.0 58.4 1.0
CA D:LEU209 5.0 58.0 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 07:45:21 2024

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