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Zinc in PDB 5sl4: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z383202616

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z383202616, PDB code: 5sl4 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) 69.24 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.713, 68.278, 138.474, 90, 90, 90
R / Rfree (%) 24.3 / 28.1

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 Z383202616 (pdb code 5sl4). 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 Z383202616, PDB code: 5sl4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sl4

Go back to Zinc Binding Sites List in 5sl4
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z383202616


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 Z383202616 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:40.0
occ:1.00
 ND1 D:HIS264 2.0 46.0 1.0
NE2 D:HIS257 2.1 41.2 1.0
SG D:CYS279 2.3 37.6 1.0
SG D:CYS261 2.4 43.8 1.0
CE1 D:HIS264 2.9 46.4 1.0
CD2 D:HIS257 2.9 40.6 1.0
CB D:CYS261 3.1 44.2 1.0
CG D:HIS264 3.1 45.8 1.0
CB D:CYS279 3.2 35.2 1.0
CE1 D:HIS257 3.2 41.2 1.0
CB D:HIS264 3.5 48.2 1.0
NE2 D:HIS264 4.0 46.6 1.0
CG D:HIS257 4.1 40.4 1.0
CD2 D:HIS264 4.2 45.8 1.0
ND1 D:HIS257 4.3 41.5 1.0
N D:HIS264 4.4 49.8 1.0
N D:ASP415 4.5 37.5 1.0
CA D:CYS261 4.5 44.9 1.0
CA D:HIS264 4.6 50.3 1.0
CA D:CYS279 4.6 34.8 1.0
CA D:CYS414 4.9 37.8 0.4
SG D:CYS414 4.9 39.3 0.6
CA D:CYS414 4.9 37.4 0.6
C D:CYS261 5.0 45.8 1.0

Zinc binding site 2 out of 3 in 5sl4

Go back to Zinc Binding Sites List in 5sl4
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z383202616


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 Z383202616 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:45.2
occ:1.00
 ND1 D:HIS487 2.1 41.9 1.0
SG D:CYS484 2.2 39.9 1.0
SG D:CYS452 2.3 48.2 1.0
SG D:CYS477 2.3 44.1 1.0
CE1 D:HIS487 3.1 41.8 1.0
CG D:HIS487 3.1 40.5 1.0
CB D:CYS477 3.2 41.0 1.0
CB D:CYS452 3.2 52.6 1.0
CB D:CYS484 3.3 39.0 1.0
CB D:HIS487 3.4 40.0 1.0
CA D:CYS452 3.8 54.3 1.0
N D:CYS484 4.0 39.2 1.0
CA D:CYS484 4.2 39.5 1.0
NE2 D:HIS487 4.2 41.8 1.0
CD2 D:HIS487 4.3 41.3 1.0
N D:CYS477 4.3 40.9 1.0
CA D:CYS477 4.4 40.6 1.0
N D:HIS487 4.4 41.0 1.0
CA D:HIS487 4.6 40.5 1.0
N D:CYS452 4.6 52.8 1.0
OG1 D:THR475 4.7 40.0 1.0
CB D:THR475 4.7 39.4 1.0
C D:CYS484 4.9 41.4 1.0
O D:CYS484 4.9 42.0 1.0
C D:CYS452 5.0 57.7 1.0
O D:HOH789 5.0 42.6 1.0

Zinc binding site 3 out of 3 in 5sl4

Go back to Zinc Binding Sites List in 5sl4
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z383202616


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 Z383202616 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:50.3
occ:1.00
 ND1 D:HIS229 2.0 47.3 1.0
SG D:CYS207 2.3 55.4 1.0
SG D:CYS210 2.4 53.7 1.0
SG D:CYS226 2.5 46.8 1.0
CE1 D:HIS229 2.9 47.8 1.0
CB D:CYS207 3.1 53.5 1.0
CG D:HIS229 3.1 45.4 1.0
CB D:CYS210 3.4 53.0 1.0
CB D:CYS226 3.4 42.5 1.0
CB D:HIS229 3.6 42.8 1.0
N D:CYS210 3.8 53.6 1.0
N D:CYS226 4.0 42.4 1.0
NE2 D:HIS229 4.1 48.2 1.0
CA D:CYS210 4.1 53.1 1.0
NH1 D:ARG212 4.1 51.8 1.0
CD2 D:HIS229 4.2 46.9 1.0
CA D:CYS226 4.3 41.7 1.0
C D:LEU209 4.4 54.5 1.0
N D:HIS229 4.4 41.4 1.0
CA D:CYS207 4.6 53.3 1.0
C D:CYS210 4.6 53.4 1.0
CB D:LEU209 4.7 54.9 1.0
CA D:HIS229 4.7 42.1 1.0
CD D:ARG212 4.7 48.9 1.0
CB D:ARG212 4.8 47.4 1.0
O D:CYS210 4.8 53.6 1.0
N D:LEU209 4.8 54.7 1.0
CA D:LEU209 4.9 54.7 1.0
CB D:HIS228 4.9 40.7 1.0
O D:LEU209 5.0 55.1 1.0
C D:CYS226 5.0 40.3 1.0
CG D:ARG212 5.0 47.6 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 07:45:22 2024

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