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Zinc in PDB 5sly: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1526504764

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1526504764, PDB code: 5sly 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) 69.29 / 2.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.76, 67.873, 138.585, 90, 90, 90
R / Rfree (%) 25.5 / 29.2

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 Z1526504764 (pdb code 5sly). 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 Z1526504764, PDB code: 5sly:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sly

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Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1526504764


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 Z1526504764 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:43.4
occ:1.00
 ND1 D:HIS264 2.0 55.6 1.0
SG D:CYS279 2.2 39.7 1.0
NE2 D:HIS257 2.2 48.3 1.0
SG D:CYS261 2.4 52.0 1.0
CE1 D:HIS264 2.9 56.0 1.0
CD2 D:HIS257 3.0 47.2 1.0
CB D:CYS261 3.0 50.8 1.0
CG D:HIS264 3.1 54.6 1.0
CB D:CYS279 3.1 39.3 1.0
CE1 D:HIS257 3.3 48.3 1.0
CB D:HIS264 3.5 55.4 1.0
NE2 D:HIS264 4.1 55.9 1.0
CG D:HIS257 4.2 46.8 1.0
CD2 D:HIS264 4.2 55.0 1.0
N D:HIS264 4.3 55.8 1.0
ND1 D:HIS257 4.3 48.5 1.0
CA D:CYS261 4.5 51.6 1.0
CA D:HIS264 4.5 56.6 1.0
CA D:CYS279 4.6 39.0 1.0
N D:ASP415 4.6 40.9 1.0
CA D:CYS414 4.9 40.5 0.4
CA D:CYS414 4.9 40.2 0.6
C D:CYS261 5.0 51.8 1.0
O D:GLY413 5.0 41.6 1.0

Zinc binding site 2 out of 3 in 5sly

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Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1526504764


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 Z1526504764 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:51.4
occ:1.00
 ND1 D:HIS487 2.3 47.4 1.0
SG D:CYS484 2.3 44.9 1.0
SG D:CYS452 2.3 60.3 1.0
SG D:CYS477 2.4 52.8 1.0
CB D:CYS477 3.2 47.6 1.0
CE1 D:HIS487 3.2 47.1 1.0
CG D:HIS487 3.3 45.4 1.0
CB D:CYS452 3.3 63.0 1.0
CB D:CYS484 3.3 46.4 1.0
CB D:HIS487 3.5 44.8 1.0
CA D:CYS452 3.9 64.2 1.0
N D:CYS484 4.0 46.6 1.0
CA D:CYS484 4.2 46.7 1.0
NE2 D:HIS487 4.4 47.4 1.0
CA D:CYS477 4.4 46.7 1.0
N D:CYS477 4.4 46.7 1.0
CD2 D:HIS487 4.4 46.7 1.0
N D:HIS487 4.4 45.3 1.0
CA D:HIS487 4.6 45.5 1.0
N D:CYS452 4.7 62.6 1.0
CB D:THR475 4.8 45.3 1.0
O D:CYS484 4.8 47.6 1.0
OG1 D:THR475 4.8 45.4 1.0
C D:CYS484 4.8 47.1 1.0
O D:HOH877 4.9 50.2 1.0

Zinc binding site 3 out of 3 in 5sly

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Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1526504764


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 Z1526504764 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:55.2
occ:1.00
 ND1 D:HIS229 2.0 53.6 1.0
SG D:CYS207 2.3 62.2 1.0
SG D:CYS210 2.3 63.1 1.0
SG D:CYS226 2.4 52.3 1.0
CE1 D:HIS229 2.8 53.9 1.0
CB D:CYS207 3.0 60.5 1.0
CG D:HIS229 3.1 51.6 1.0
CB D:CYS210 3.4 61.4 1.0
CB D:CYS226 3.5 48.2 1.0
CB D:HIS229 3.6 49.4 1.0
N D:CYS210 3.8 61.5 1.0
N D:CYS226 3.9 47.6 1.0
NE2 D:HIS229 4.0 53.7 1.0
CA D:CYS210 4.1 61.2 1.0
CD2 D:HIS229 4.2 52.6 1.0
CA D:CYS226 4.3 47.1 1.0
N D:HIS229 4.3 48.8 1.0
NH1 D:ARG212 4.4 61.4 1.0
C D:LEU209 4.4 62.2 1.0
CA D:CYS207 4.5 60.5 1.0
CA D:HIS229 4.6 48.7 1.0
C D:CYS210 4.6 61.2 1.0
CB D:LEU209 4.7 63.0 1.0
CD D:ARG212 4.8 56.9 1.0
N D:LEU209 4.8 62.2 1.0
CA D:LEU209 4.8 62.4 1.0
O D:CYS210 4.9 61.7 1.0
C D:CYS226 4.9 46.2 1.0
CB D:HIS228 4.9 48.3 1.0
CB D:ARG212 4.9 56.1 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 07:56:57 2024

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