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Zinc in PDB 5slf: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z198195770

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z198195770, PDB code: 5slf 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) 69.17 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.606, 67.764, 138.339, 90, 90, 90
R / Rfree (%) 20.2 / 24.5

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 Z198195770 (pdb code 5slf). 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 Z198195770, PDB code: 5slf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slf

Go back to Zinc Binding Sites List in 5slf
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:31.6
occ:1.00
 ND1 D:HIS264 1.9 29.4 1.0
NE2 D:HIS257 2.0 41.2 1.0
SG D:CYS279 2.3 28.1 1.0
SG D:CYS261 2.4 37.4 1.0
CE1 D:HIS264 2.7 30.9 1.0
CG D:HIS264 3.0 32.9 1.0
CD2 D:HIS257 3.0 39.2 1.0
CE1 D:HIS257 3.0 39.5 1.0
CB D:CYS279 3.1 29.2 1.0
CB D:CYS261 3.1 37.5 1.0
CB D:HIS264 3.5 40.4 1.0
NE2 D:HIS264 3.9 31.2 1.0
CD2 D:HIS264 4.0 30.5 1.0
ND1 D:HIS257 4.1 41.1 1.0
CG D:HIS257 4.1 39.8 1.0
N D:HIS264 4.4 42.5 1.0
CA D:CYS261 4.5 39.7 1.0
CA D:CYS279 4.6 29.1 1.0
CA D:HIS264 4.6 43.6 1.0
N D:ASP415 4.6 32.0 1.0
O D:HOH778 4.9 41.3 1.0
C D:CYS261 5.0 40.3 1.0
CA D:CYS414 5.0 34.7 0.6

Zinc binding site 2 out of 3 in 5slf

Go back to Zinc Binding Sites List in 5slf
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:37.9
occ:1.00
 ND1 D:HIS487 2.2 37.4 1.0
SG D:CYS484 2.2 39.5 1.0
SG D:CYS452 2.3 44.3 1.0
SG D:CYS477 2.4 35.8 1.0
CG D:HIS487 3.1 33.6 1.0
CB D:CYS452 3.1 48.1 1.0
CB D:CYS477 3.1 39.3 1.0
CE1 D:HIS487 3.2 36.5 1.0
CB D:CYS484 3.3 36.7 1.0
CB D:HIS487 3.4 33.6 1.0
CA D:CYS452 3.7 52.6 1.0
N D:CYS484 4.0 33.5 1.0
CA D:CYS484 4.2 35.6 1.0
CD2 D:HIS487 4.3 35.5 1.0
NE2 D:HIS487 4.3 34.3 1.0
CA D:CYS477 4.4 37.3 1.0
N D:CYS452 4.4 49.9 1.0
N D:CYS477 4.4 37.1 1.0
N D:HIS487 4.5 39.6 1.0
CA D:HIS487 4.5 37.9 1.0
CB D:THR475 4.7 36.7 1.0
O D:CYS484 4.8 42.2 1.0
C D:CYS484 4.8 41.4 1.0
OG1 D:THR475 4.8 34.2 1.0
O D:HOH806 5.0 36.0 1.0

Zinc binding site 3 out of 3 in 5slf

Go back to Zinc Binding Sites List in 5slf
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:42.1
occ:1.00
 ND1 D:HIS229 1.8 41.4 1.0
SG D:CYS210 2.3 44.0 1.0
SG D:CYS207 2.3 44.5 1.0
SG D:CYS226 2.5 41.4 1.0
CE1 D:HIS229 2.6 42.4 1.0
CB D:CYS207 2.9 40.6 1.0
CG D:HIS229 3.0 37.6 1.0
CB D:CYS210 3.5 44.8 1.0
CB D:HIS229 3.5 37.3 1.0
CB D:CYS226 3.6 39.9 1.0
N D:CYS210 3.8 43.4 1.0
NE2 D:HIS229 3.8 40.6 1.0
N D:CYS226 4.0 38.1 1.0
CD2 D:HIS229 4.0 37.5 1.0
NH1 D:ARG212 4.1 47.0 1.0
CA D:CYS210 4.1 42.5 1.0
CA D:CYS226 4.4 36.2 1.0
CA D:CYS207 4.4 45.8 1.0
C D:LEU209 4.4 45.6 1.0
N D:HIS229 4.6 38.4 1.0
CB D:ARG212 4.6 48.1 1.0
CB D:LEU209 4.6 47.7 1.0
C D:CYS210 4.7 42.4 1.0
CA D:HIS229 4.7 36.0 1.0
CB D:HIS228 4.7 37.1 1.0
CD D:ARG212 4.8 42.4 1.0
N D:LEU209 4.8 49.2 1.0
CA D:LEU209 4.9 47.1 1.0
O D:CYS210 4.9 49.0 1.0
CG D:ARG212 4.9 43.6 1.0
C D:CYS226 5.0 34.5 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 07:48:56 2024

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