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Zinc in PDB 5sl3: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z223688272

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z223688272, PDB code: 5sl3 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) 69.25 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.66, 68.344, 138.49, 90, 90, 90
R / Rfree (%) 24 / 26.9

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 Z223688272 (pdb code 5sl3). 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 Z223688272, PDB code: 5sl3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sl3

Go back to Zinc Binding Sites List in 5sl3
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z223688272


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 Z223688272 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:36.4
occ:1.00
 ND1 D:HIS264 1.9 45.8 1.0
NE2 D:HIS257 2.2 41.1 1.0
SG D:CYS279 2.3 33.4 1.0
SG D:CYS261 2.4 42.4 1.0
CE1 D:HIS264 2.8 46.4 1.0
CD2 D:HIS257 3.1 39.8 1.0
CG D:HIS264 3.1 45.3 1.0
CB D:CYS261 3.1 43.8 1.0
CB D:CYS279 3.1 31.9 1.0
CE1 D:HIS257 3.2 41.0 1.0
CB D:HIS264 3.5 47.1 1.0
NE2 D:HIS264 4.0 46.2 1.0
CD2 D:HIS264 4.1 45.5 1.0
CG D:HIS257 4.2 39.4 1.0
ND1 D:HIS257 4.2 40.8 1.0
N D:HIS264 4.3 49.0 1.0
CA D:HIS264 4.5 49.0 1.0
N D:ASP415 4.5 33.9 1.0
CA D:CYS261 4.6 45.0 1.0
CA D:CYS279 4.6 31.5 1.0
CA D:CYS414 4.9 33.7 0.4
CA D:CYS414 4.9 34.3 0.6
C D:CYS261 5.0 45.8 1.0

Zinc binding site 2 out of 3 in 5sl3

Go back to Zinc Binding Sites List in 5sl3
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z223688272


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 Z223688272 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:41.5
occ:1.00
 ND1 D:HIS487 2.2 35.9 1.0
SG D:CYS484 2.2 37.5 1.0
SG D:CYS477 2.3 39.8 1.0
SG D:CYS452 2.4 46.2 1.0
CG D:HIS487 3.2 34.8 1.0
CE1 D:HIS487 3.2 35.9 1.0
CB D:CYS484 3.2 37.8 1.0
CB D:CYS477 3.2 36.8 1.0
CB D:CYS452 3.3 50.7 1.0
CB D:HIS487 3.4 34.8 1.0
CA D:CYS452 3.8 52.4 1.0
N D:CYS484 4.0 38.4 1.0
CA D:CYS484 4.1 38.1 1.0
NE2 D:HIS487 4.3 36.4 1.0
CD2 D:HIS487 4.3 35.5 1.0
N D:HIS487 4.4 36.9 1.0
N D:CYS477 4.4 37.4 1.0
CA D:CYS477 4.4 36.6 1.0
CA D:HIS487 4.5 36.0 1.0
N D:CYS452 4.7 50.6 1.0
CB D:THR475 4.8 36.2 1.0
C D:CYS484 4.8 38.8 1.0
O D:CYS484 4.8 38.5 1.0
OG1 D:THR475 4.9 36.6 1.0

Zinc binding site 3 out of 3 in 5sl3

Go back to Zinc Binding Sites List in 5sl3
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z223688272


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 Z223688272 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:48.0
occ:1.00
 ND1 D:HIS229 2.0 46.2 1.0
SG D:CYS207 2.3 54.8 1.0
SG D:CYS210 2.4 52.5 1.0
SG D:CYS226 2.4 45.3 1.0
CE1 D:HIS229 2.7 46.8 1.0
CB D:CYS207 3.0 52.6 1.0
CG D:HIS229 3.2 44.4 1.0
CB D:CYS210 3.4 51.2 1.0
CB D:CYS226 3.4 41.0 1.0
CB D:HIS229 3.7 42.5 1.0
N D:CYS210 3.8 51.5 1.0
N D:CYS226 3.9 41.4 1.0
NE2 D:HIS229 4.0 47.1 1.0
CA D:CYS210 4.1 51.2 1.0
CD2 D:HIS229 4.2 45.9 1.0
CA D:CYS226 4.3 40.0 1.0
NH1 D:ARG212 4.3 45.9 1.0
C D:LEU209 4.4 52.1 1.0
N D:HIS229 4.4 41.0 1.0
CA D:CYS207 4.5 52.6 1.0
C D:CYS210 4.7 51.3 1.0
CB D:LEU209 4.7 52.7 1.0
CD D:ARG212 4.7 46.1 1.0
CA D:HIS229 4.8 41.7 1.0
CB D:ARG212 4.8 45.6 1.0
N D:LEU209 4.8 52.6 1.0
CA D:LEU209 4.9 52.3 1.0
CB D:HIS228 4.9 39.3 1.0
O D:CYS210 5.0 51.4 1.0
O D:LEU209 5.0 52.8 1.0
C D:CYS226 5.0 38.2 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: Fri Apr 7 23:18:18 2023

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