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Zinc in PDB 5sm5: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434807

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434807, PDB code: 5sm5 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) 69.20 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.774, 68.054, 138.403, 90, 90, 90
R / Rfree (%) 20.4 / 24.9

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 Z2856434807 (pdb code 5sm5). 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 Z2856434807, PDB code: 5sm5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sm5

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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 Z2856434807


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 Z2856434807 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:33.8
occ:1.00
 ND1 D:HIS264 2.0 33.3 1.0
NE2 D:HIS257 2.1 36.8 1.0
SG D:CYS279 2.2 28.4 1.0
SG D:CYS261 2.4 36.2 1.0
CE1 D:HIS264 2.9 34.3 1.0
CD2 D:HIS257 3.0 37.7 1.0
CG D:HIS264 3.0 35.7 1.0
CB D:CYS261 3.1 38.3 1.0
CB D:CYS279 3.1 27.4 1.0
CE1 D:HIS257 3.1 37.4 1.0
CB D:HIS264 3.4 40.3 1.0
NE2 D:HIS264 4.1 36.7 1.0
CD2 D:HIS264 4.1 33.3 1.0
CG D:HIS257 4.2 40.9 1.0
ND1 D:HIS257 4.2 39.8 1.0
N D:HIS264 4.3 39.0 1.0
CA D:HIS264 4.5 42.5 1.0
CA D:CYS261 4.5 39.2 1.0
CA D:CYS279 4.6 29.0 1.0
N D:ASP415 4.6 32.1 1.0
O D:HOH770 4.9 38.0 1.0
C D:CYS261 5.0 41.4 1.0
CA D:CYS414 5.0 34.7 0.6

Zinc binding site 2 out of 3 in 5sm5

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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 Z2856434807


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 Z2856434807 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:37.6
occ:1.00
 ND1 D:HIS487 2.2 34.7 1.0
SG D:CYS484 2.2 35.6 1.0
SG D:CYS452 2.3 44.4 1.0
SG D:CYS477 2.4 35.4 1.0
CB D:CYS452 3.1 47.2 1.0
CE1 D:HIS487 3.2 33.6 1.0
CG D:HIS487 3.2 33.9 1.0
CB D:CYS477 3.2 36.6 1.0
CB D:CYS484 3.2 36.8 1.0
CB D:HIS487 3.5 33.5 1.0
CA D:CYS452 3.7 51.5 1.0
N D:CYS484 4.0 34.1 1.0
CA D:CYS484 4.2 36.0 1.0
NE2 D:HIS487 4.3 33.8 1.0
CD2 D:HIS487 4.3 34.2 1.0
N D:CYS477 4.4 37.3 1.0
CA D:CYS477 4.4 36.3 1.0
N D:CYS452 4.4 47.8 1.0
N D:HIS487 4.5 36.0 1.0
CA D:HIS487 4.6 37.1 1.0
CB D:THR475 4.7 36.6 1.0
O D:CYS484 4.8 41.1 1.0
C D:CYS484 4.8 39.9 1.0
OG1 D:THR475 4.8 36.3 1.0
C D:CYS452 5.0 52.1 1.0

Zinc binding site 3 out of 3 in 5sm5

Go back to Zinc Binding Sites List in 5sm5
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434807


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 Z2856434807 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:43.7
occ:1.00
 ND1 D:HIS229 1.9 40.6 1.0
SG D:CYS207 2.3 47.9 1.0
SG D:CYS210 2.4 45.6 1.0
SG D:CYS226 2.4 41.1 1.0
CE1 D:HIS229 2.7 42.6 1.0
CB D:CYS207 2.9 42.4 1.0
CG D:HIS229 3.1 36.2 1.0
CB D:CYS210 3.4 47.1 1.0
CB D:CYS226 3.5 39.4 1.0
CB D:HIS229 3.6 39.1 1.0
N D:CYS210 3.8 49.3 1.0
NE2 D:HIS229 3.9 41.6 1.0
N D:CYS226 3.9 38.9 1.0
CA D:CYS210 4.1 45.5 1.0
CD2 D:HIS229 4.1 38.5 1.0
CA D:CYS226 4.3 36.3 1.0
NH1 D:ARG212 4.4 52.1 1.0
CA D:CYS207 4.4 46.3 1.0
C D:LEU209 4.4 49.6 1.0
N D:HIS229 4.6 36.3 1.0
C D:CYS210 4.6 45.7 1.0
CB D:ARG212 4.7 49.7 1.0
CD D:ARG212 4.7 46.2 1.0
CB D:LEU209 4.7 49.6 1.0
CA D:HIS229 4.8 37.0 1.0
N D:LEU209 4.8 51.3 1.0
CB D:HIS228 4.9 35.3 1.0
CA D:LEU209 4.9 49.8 1.0
CG D:ARG212 4.9 44.3 1.0
C D:CYS226 5.0 34.4 1.0
O D:CYS210 5.0 51.5 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 07:59:58 2024

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