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Zinc in PDB 5sl0: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57260516

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57260516, PDB code: 5sl0 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) 69.26 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.878, 68.365, 138.528, 90, 90, 90
R / Rfree (%) 22.4 / 26

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 Z57260516 (pdb code 5sl0). 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 Z57260516, PDB code: 5sl0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sl0

Go back to Zinc Binding Sites List in 5sl0
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57260516


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 Z57260516 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:35.3
occ:1.00
 ND1 D:HIS264 1.9 38.2 1.0
NE2 D:HIS257 2.2 36.8 1.0
SG D:CYS279 2.3 34.8 1.0
SG D:CYS261 2.4 40.0 1.0
CE1 D:HIS264 2.8 39.1 1.0
CD2 D:HIS257 3.0 35.8 1.0
CG D:HIS264 3.1 38.4 1.0
CB D:CYS261 3.1 40.8 1.0
CB D:CYS279 3.2 32.4 1.0
CE1 D:HIS257 3.2 36.9 1.0
CB D:HIS264 3.5 42.7 1.0
NE2 D:HIS264 4.0 39.0 1.0
CD2 D:HIS264 4.1 38.1 1.0
CG D:HIS257 4.2 35.8 1.0
ND1 D:HIS257 4.3 37.1 1.0
N D:HIS264 4.4 45.2 1.0
N D:ASP415 4.5 34.6 1.0
CA D:CYS261 4.6 42.2 1.0
CA D:HIS264 4.6 45.9 1.0
CA D:CYS279 4.6 32.0 1.0
SG D:CYS414 4.9 38.0 0.6
O D:HOH782 4.9 37.2 1.0
CA D:CYS414 4.9 33.7 0.6
CA D:CYS414 4.9 33.2 0.4
C D:CYS261 5.0 42.0 1.0

Zinc binding site 2 out of 3 in 5sl0

Go back to Zinc Binding Sites List in 5sl0
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57260516


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 Z57260516 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:40.5
occ:1.00
 ND1 D:HIS487 2.1 37.5 1.0
SG D:CYS484 2.3 40.5 1.0
SG D:CYS452 2.3 47.0 1.0
SG D:CYS477 2.4 36.1 1.0
CE1 D:HIS487 3.1 37.2 1.0
CG D:HIS487 3.1 35.4 1.0
CB D:CYS452 3.2 49.7 1.0
CB D:CYS484 3.3 39.9 1.0
CB D:CYS477 3.3 35.1 1.0
CB D:HIS487 3.4 35.1 1.0
CA D:CYS452 3.8 51.2 1.0
N D:CYS484 4.0 39.5 1.0
CA D:CYS484 4.2 39.5 1.0
NE2 D:HIS487 4.2 37.0 1.0
CD2 D:HIS487 4.2 36.1 1.0
N D:HIS487 4.4 36.7 1.0
N D:CYS477 4.4 36.2 1.0
CA D:CYS477 4.5 35.5 1.0
CA D:HIS487 4.5 35.4 1.0
N D:CYS452 4.5 49.8 1.0
OG1 D:THR475 4.6 36.0 1.0
CB D:THR475 4.7 34.6 1.0
O D:CYS484 4.8 40.0 1.0
C D:CYS484 4.8 39.6 1.0

Zinc binding site 3 out of 3 in 5sl0

Go back to Zinc Binding Sites List in 5sl0
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57260516


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 Z57260516 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:46.2
occ:1.00
 ND1 D:HIS229 2.0 45.9 1.0
SG D:CYS207 2.2 44.7 1.0
SG D:CYS210 2.3 51.5 1.0
SG D:CYS226 2.4 41.1 1.0
CE1 D:HIS229 2.8 46.4 1.0
CB D:CYS207 3.0 47.1 1.0
CG D:HIS229 3.2 43.8 1.0
CB D:CYS210 3.4 50.1 1.0
CB D:CYS226 3.5 38.6 1.0
CB D:HIS229 3.7 41.2 1.0
N D:CYS210 3.8 50.4 1.0
N D:CYS226 4.0 37.9 1.0
CA D:CYS210 4.0 49.8 1.0
NE2 D:HIS229 4.1 46.1 1.0
CD2 D:HIS229 4.2 45.2 1.0
C D:LEU209 4.3 51.6 1.0
CA D:CYS226 4.3 37.6 1.0
NH1 D:ARG212 4.4 48.7 1.0
N D:HIS229 4.4 40.0 1.0
CA D:CYS207 4.5 48.2 1.0
C D:CYS210 4.6 49.6 1.0
CA D:HIS229 4.7 40.2 1.0
CD D:ARG212 4.7 46.2 1.0
N D:LEU209 4.8 51.9 1.0
CB D:LEU209 4.8 52.7 1.0
CB D:ARG212 4.8 43.8 1.0
CA D:LEU209 4.8 52.0 1.0
O D:CYS210 4.9 50.0 1.0
CB D:HIS228 4.9 39.8 1.0
O D:LEU209 4.9 52.3 1.0
C D:CYS226 4.9 37.2 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 07:43:22 2024

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