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Zinc in PDB 5sm6: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1899842917

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1899842917, PDB code: 5sm6 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) 68.98 / 2.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.36, 67.97, 137.96, 90, 90, 90
R / Rfree (%) 22.9 / 27.8

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 Z1899842917 (pdb code 5sm6). 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 Z1899842917, PDB code: 5sm6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sm6

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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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:49.0
occ:1.00
 ND1 D:HIS264 1.9 56.6 1.0
NE2 D:HIS257 2.1 56.0 1.0
SG D:CYS279 2.3 43.3 1.0
SG D:CYS261 2.4 55.9 1.0
CE1 D:HIS264 2.8 57.0 1.0
CD2 D:HIS257 3.0 55.3 1.0
CB D:CYS261 3.0 54.5 1.0
CG D:HIS264 3.1 55.6 1.0
CE1 D:HIS257 3.2 55.8 1.0
CB D:CYS279 3.2 43.4 1.0
CB D:HIS264 3.5 56.8 1.0
NE2 D:HIS264 4.0 56.9 1.0
CG D:HIS257 4.1 54.3 1.0
CD2 D:HIS264 4.1 56.0 1.0
ND1 D:HIS257 4.2 55.5 1.0
N D:HIS264 4.4 57.2 1.0
CA D:CYS261 4.5 54.9 1.0
CA D:HIS264 4.6 58.1 1.0
CA D:CYS279 4.6 44.2 1.0
N D:ASP415 4.7 47.7 1.0
O D:HOH807 4.8 52.7 1.0
SG D:CYS414 4.8 47.1 0.6
C D:CYS261 4.9 55.5 1.0
CA D:MET276 4.9 43.7 1.0
CA D:CYS414 5.0 47.7 0.4

Zinc binding site 2 out of 3 in 5sm6

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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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:57.4
occ:1.00
 SG D:CYS484 2.2 52.7 1.0
ND1 D:HIS487 2.3 53.8 1.0
SG D:CYS452 2.3 68.4 1.0
SG D:CYS477 2.4 57.1 1.0
CB D:CYS452 3.1 69.3 1.0
CB D:CYS477 3.2 53.8 1.0
CE1 D:HIS487 3.2 53.9 1.0
CB D:CYS484 3.3 54.0 1.0
CG D:HIS487 3.3 52.4 1.0
CB D:HIS487 3.7 51.8 1.0
CA D:CYS452 3.7 70.4 1.0
N D:CYS484 4.0 54.6 1.0
CA D:CYS484 4.2 54.4 1.0
NE2 D:HIS487 4.3 54.1 1.0
CA D:CYS477 4.4 53.5 1.0
N D:CYS477 4.4 54.1 1.0
CD2 D:HIS487 4.4 53.4 1.0
N D:HIS487 4.5 51.6 1.0
N D:CYS452 4.6 69.3 1.0
CA D:HIS487 4.7 52.0 1.0
CB D:THR475 4.8 54.0 1.0
OG1 D:THR475 4.8 55.4 1.0
O D:CYS484 4.8 55.4 1.0
C D:CYS484 4.8 54.9 1.0
C D:CYS452 4.9 73.0 1.0
O D:HOH751 5.0 41.6 1.0

Zinc binding site 3 out of 3 in 5sm6

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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 Z1899842917


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 Z1899842917 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:59.6
occ:1.00
 ND1 D:HIS229 1.9 62.3 1.0
SG D:CYS207 2.2 64.8 1.0
SG D:CYS210 2.4 69.5 1.0
SG D:CYS226 2.5 60.5 1.0
CE1 D:HIS229 2.7 62.7 1.0
CB D:CYS207 3.0 62.9 1.0
CG D:HIS229 3.1 60.3 1.0
CB D:CYS210 3.3 65.9 1.0
CB D:CYS226 3.4 56.1 1.0
N D:CYS210 3.7 65.6 1.0
CB D:HIS229 3.7 57.0 1.0
N D:CYS226 3.9 55.3 1.0
NE2 D:HIS229 3.9 62.5 1.0
CA D:CYS210 4.0 65.5 1.0
CD2 D:HIS229 4.1 61.4 1.0
CA D:CYS226 4.2 55.1 1.0
N D:HIS229 4.4 55.4 1.0
C D:LEU209 4.4 66.3 1.0
NH1 D:ARG212 4.4 66.2 1.0
CA D:CYS207 4.4 62.8 1.0
C D:CYS210 4.5 65.6 1.0
CA D:HIS229 4.7 55.7 1.0
CB D:LEU209 4.7 67.0 1.0
N D:LEU209 4.8 66.1 1.0
CD D:ARG212 4.8 62.5 1.0
CA D:LEU209 4.9 66.4 1.0
CB D:ARG212 4.9 60.2 1.0
O D:CYS210 4.9 65.9 1.0
C D:CYS226 5.0 54.6 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 07:59:58 2024

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