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Zinc in PDB 5smh: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434938

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434938, PDB code: 5smh 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 / 2.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.99, 68.41, 138.38, 90, 90, 90
R / Rfree (%) 21.1 / 28

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 Z2856434938 (pdb code 5smh). 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 Z2856434938, PDB code: 5smh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5smh

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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 Z2856434938


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 Z2856434938 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:42.6
occ:1.00
 ND1 D:HIS264 2.0 51.2 1.0
NE2 D:HIS257 2.1 43.1 1.0
SG D:CYS279 2.2 35.6 1.0
SG D:CYS261 2.3 47.0 1.0
CE1 D:HIS264 2.9 51.9 1.0
CB D:CYS261 3.0 47.5 1.0
CD2 D:HIS257 3.0 42.6 1.0
CG D:HIS264 3.1 49.7 1.0
CE1 D:HIS257 3.1 43.1 1.0
CB D:CYS279 3.3 34.3 1.0
CB D:HIS264 3.5 50.0 1.0
NE2 D:HIS264 4.0 51.9 1.0
CD2 D:HIS264 4.1 50.6 1.0
CG D:HIS257 4.2 42.2 1.0
ND1 D:HIS257 4.2 43.1 1.0
N D:HIS264 4.2 50.8 1.0
N D:ASP415 4.4 42.0 1.0
CA D:CYS261 4.4 47.9 1.0
CA D:HIS264 4.5 51.2 1.0
CA D:CYS279 4.7 34.7 1.0
CA D:CYS414 4.8 41.8 0.4
C D:CYS261 4.8 48.8 1.0
CA D:CYS414 4.9 42.6 0.6
SG D:CYS414 4.9 49.9 0.6
O D:HOH799 4.9 39.6 1.0

Zinc binding site 2 out of 3 in 5smh

Go back to Zinc Binding Sites List in 5smh
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434938


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 Z2856434938 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:47.5
occ:1.00
 SG D:CYS484 2.2 42.6 1.0
ND1 D:HIS487 2.2 48.8 1.0
SG D:CYS452 2.3 58.4 1.0
SG D:CYS477 2.4 46.1 1.0
CE1 D:HIS487 3.2 49.1 1.0
CB D:CYS477 3.2 41.5 1.0
CG D:HIS487 3.3 46.8 1.0
CB D:CYS484 3.3 43.2 1.0
CB D:CYS452 3.3 56.9 1.0
CB D:HIS487 3.6 44.6 1.0
CA D:CYS452 3.9 56.8 1.0
N D:CYS484 3.9 45.0 1.0
CA D:CYS484 4.2 43.8 1.0
NE2 D:HIS487 4.3 48.8 1.0
N D:CYS477 4.4 41.1 1.0
CD2 D:HIS487 4.4 47.7 1.0
CA D:CYS477 4.4 40.8 1.0
N D:HIS487 4.5 44.3 1.0
N D:CYS452 4.5 55.3 1.0
CA D:HIS487 4.6 44.4 1.0
CB D:THR475 4.8 41.8 1.0
OG1 D:THR475 4.8 42.5 1.0
O D:CYS484 4.8 44.1 1.0
C D:CYS484 4.8 44.1 1.0

Zinc binding site 3 out of 3 in 5smh

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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 Z2856434938


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 Z2856434938 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:52.4
occ:1.00
 ND1 D:HIS229 2.1 45.9 1.0
SG D:CYS207 2.2 50.7 1.0
SG D:CYS210 2.3 51.7 1.0
SG D:CYS226 2.5 46.5 1.0
CE1 D:HIS229 2.7 46.5 1.0
CB D:CYS207 2.8 49.3 1.0
CG D:HIS229 3.4 44.5 1.0
CB D:CYS210 3.4 48.3 1.0
CB D:CYS226 3.5 42.3 1.0
N D:CYS210 3.7 48.1 1.0
NH1 D:ARG212 3.8 53.9 1.0
N D:CYS226 3.9 41.8 1.0
CA D:CYS210 4.0 48.1 1.0
CB D:HIS229 4.0 43.5 1.0
NE2 D:HIS229 4.0 46.5 1.0
CA D:CYS207 4.3 49.3 1.0
CD2 D:HIS229 4.3 45.5 1.0
CA D:CYS226 4.4 41.5 1.0
C D:LEU209 4.4 48.5 1.0
C D:CYS210 4.5 48.4 1.0
N D:HIS229 4.6 43.2 1.0
CB D:ARG212 4.7 46.1 1.0
N D:LEU209 4.8 49.4 1.0
O D:CYS210 4.8 48.5 1.0
C D:CYS207 4.8 50.4 1.0
CB D:LEU209 4.9 49.3 1.0
CB D:HIS228 4.9 43.3 1.0
CA D:LEU209 4.9 48.9 1.0
N D:ARG212 5.0 45.7 1.0
CA D:HIS229 5.0 43.5 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 08:02:58 2024

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