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Zinc in PDB 5slb: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z744930860

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z744930860, PDB code: 5slb 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) 69.19 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.678, 68.3, 138.375, 90, 90, 90
R / Rfree (%) 22.5 / 24.2

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 Z744930860 (pdb code 5slb). 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 Z744930860, PDB code: 5slb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slb

Go back to Zinc Binding Sites List in 5slb
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z744930860


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 Z744930860 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:33.3
occ:1.00
 ND1 D:HIS264 2.0 36.9 1.0
NE2 D:HIS257 2.1 35.9 1.0
SG D:CYS279 2.2 31.8 1.0
SG D:CYS261 2.4 35.4 1.0
CD2 D:HIS257 2.9 35.1 1.0
CE1 D:HIS264 2.9 37.6 1.0
CB D:CYS279 3.1 29.3 1.0
CG D:HIS264 3.1 37.1 1.0
CB D:CYS261 3.1 37.5 1.0
CE1 D:HIS257 3.1 35.8 1.0
CB D:HIS264 3.5 40.9 1.0
CG D:HIS257 4.1 34.9 1.0
NE2 D:HIS264 4.1 37.8 1.0
ND1 D:HIS257 4.2 35.6 1.0
CD2 D:HIS264 4.2 36.9 1.0
N D:HIS264 4.4 43.4 1.0
CA D:CYS279 4.5 28.9 1.0
N D:ASP415 4.6 33.7 1.0
CA D:CYS261 4.6 39.0 1.0
CA D:HIS264 4.6 43.8 1.0
O D:HOH789 4.9 34.4 1.0
SG D:CYS414 4.9 38.5 0.6
CA D:CYS414 5.0 32.8 0.6

Zinc binding site 2 out of 3 in 5slb

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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 Z744930860


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 Z744930860 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:36.3
occ:1.00
 ND1 D:HIS487 2.1 34.5 1.0
SG D:CYS484 2.3 38.1 1.0
SG D:CYS452 2.3 41.5 1.0
SG D:CYS477 2.4 33.6 1.0
CE1 D:HIS487 3.1 34.8 1.0
CG D:HIS487 3.1 32.7 1.0
CB D:CYS452 3.2 44.5 1.0
CB D:CYS477 3.2 33.4 1.0
CB D:CYS484 3.3 35.4 1.0
CB D:HIS487 3.4 31.9 1.0
CA D:CYS452 3.8 46.0 1.0
N D:CYS484 4.0 34.9 1.0
CA D:CYS484 4.2 35.1 1.0
NE2 D:HIS487 4.2 34.4 1.0
CD2 D:HIS487 4.2 33.4 1.0
N D:CYS477 4.4 34.2 1.0
CA D:CYS477 4.4 33.7 1.0
N D:HIS487 4.4 32.7 1.0
CA D:HIS487 4.5 32.1 1.0
N D:CYS452 4.6 44.6 1.0
OG1 D:THR475 4.6 33.6 1.0
CB D:THR475 4.7 32.4 1.0
O D:CYS484 4.9 35.4 1.0
C D:CYS484 4.9 35.9 1.0
C D:CYS452 5.0 49.2 1.0

Zinc binding site 3 out of 3 in 5slb

Go back to Zinc Binding Sites List in 5slb
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z744930860


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 Z744930860 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:44.5
occ:1.00
 ND1 D:HIS229 2.0 44.8 1.0
SG D:CYS207 2.3 45.0 1.0
SG D:CYS210 2.4 48.7 1.0
SG D:CYS226 2.5 42.3 1.0
CE1 D:HIS229 2.8 45.5 1.0
CB D:CYS207 3.0 45.2 1.0
CG D:HIS229 3.2 42.7 1.0
CB D:CYS210 3.4 48.3 1.0
CB D:CYS226 3.5 38.0 1.0
CB D:HIS229 3.7 39.4 1.0
N D:CYS210 3.8 49.1 1.0
N D:CYS226 4.0 36.7 1.0
NE2 D:HIS229 4.1 45.6 1.0
CA D:CYS210 4.1 48.5 1.0
NH1 D:ARG212 4.2 46.5 1.0
CD2 D:HIS229 4.2 44.5 1.0
CA D:CYS226 4.4 36.2 1.0
C D:LEU209 4.4 50.2 1.0
N D:HIS229 4.5 38.0 1.0
CA D:CYS207 4.5 45.9 1.0
C D:CYS210 4.6 48.7 1.0
CD D:ARG212 4.7 42.9 1.0
CB D:LEU209 4.7 50.6 1.0
CA D:HIS229 4.8 38.3 1.0
CB D:ARG212 4.8 41.6 1.0
N D:LEU209 4.8 50.1 1.0
O D:CYS210 4.8 49.2 1.0
CA D:LEU209 4.8 50.2 1.0
CB D:HIS228 4.9 37.6 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 07:47:53 2024

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