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Zinc in PDB 5sl1: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1273312153

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1273312153, PDB code: 5sl1 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) 27.88 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.247, 67.418, 138.738, 90, 90, 90
R / Rfree (%) 20.5 / 26.7

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 Z1273312153 (pdb code 5sl1). 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 Z1273312153, PDB code: 5sl1:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sl1

Go back to Zinc Binding Sites List in 5sl1
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:41.6
occ:1.00
 ND1 D:HIS264 2.0 44.8 1.0
NE2 D:HIS257 2.2 40.9 1.0
SG D:CYS279 2.2 34.5 1.0
SG D:CYS261 2.4 44.3 1.0
CE1 D:HIS264 2.9 45.4 1.0
CB D:CYS261 3.0 44.8 1.0
CE1 D:HIS257 3.1 41.0 1.0
CD2 D:HIS257 3.1 41.1 1.0
CG D:HIS264 3.2 44.2 1.0
CB D:CYS279 3.2 35.4 1.0
CB D:HIS264 3.6 45.8 1.0
NE2 D:HIS264 4.1 45.4 1.0
CD2 D:HIS264 4.2 44.7 1.0
ND1 D:HIS257 4.2 41.4 1.0
CG D:HIS257 4.2 40.8 1.0
N D:HIS264 4.3 47.0 1.0
CA D:CYS261 4.4 45.8 1.0
N D:ASP415 4.5 37.2 1.0
CA D:HIS264 4.6 47.6 1.0
CA D:CYS279 4.6 36.5 1.0
CA D:CYS414 4.8 35.9 0.4
O D:HOH813 4.8 40.7 1.0
SG D:CYS414 4.8 40.1 0.6
CA D:CYS414 4.9 36.8 0.6
C D:CYS261 4.9 46.2 1.0

Zinc binding site 2 out of 3 in 5sl1

Go back to Zinc Binding Sites List in 5sl1
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:47.8
occ:1.00
 ND1 D:HIS487 2.2 43.8 1.0
SG D:CYS484 2.2 44.5 1.0
SG D:CYS452 2.5 57.2 1.0
SG D:CYS477 2.5 46.6 1.0
CE1 D:HIS487 3.1 43.9 1.0
CB D:CYS477 3.2 42.6 1.0
CG D:HIS487 3.3 41.8 1.0
CB D:CYS452 3.3 58.2 1.0
CB D:CYS484 3.4 44.0 1.0
CB D:HIS487 3.6 40.8 1.0
CA D:CYS452 3.9 59.2 1.0
N D:CYS484 4.0 45.0 1.0
CA D:CYS484 4.3 44.1 1.0
NE2 D:HIS487 4.3 43.5 1.0
CD2 D:HIS487 4.4 42.5 1.0
N D:CYS477 4.4 42.4 1.0
CA D:CYS477 4.5 42.2 1.0
N D:HIS487 4.6 41.3 1.0
N D:CYS452 4.6 57.8 1.0
CB D:THR475 4.7 40.0 1.0
CA D:HIS487 4.7 40.8 1.0
OG1 D:THR475 4.8 40.8 1.0
O D:CYS484 4.9 44.3 1.0
C D:CYS484 4.9 44.1 1.0
O D:HOH820 4.9 34.9 1.0

Zinc binding site 3 out of 3 in 5sl1

Go back to Zinc Binding Sites List in 5sl1
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:49.8
occ:1.00
 ND1 D:HIS229 2.0 48.0 1.0
SG D:CYS207 2.3 51.7 1.0
SG D:CYS210 2.4 54.5 1.0
SG D:CYS226 2.6 48.0 1.0
CE1 D:HIS229 2.8 48.7 1.0
CB D:CYS207 2.9 52.2 1.0
CG D:HIS229 3.2 46.2 1.0
CB D:CYS210 3.5 52.4 1.0
CB D:CYS226 3.5 43.7 1.0
CB D:HIS229 3.7 43.9 1.0
N D:CYS210 3.8 52.6 1.0
N D:CYS226 4.0 42.0 1.0
NE2 D:HIS229 4.0 48.4 1.0
CA D:CYS210 4.1 52.3 1.0
CD2 D:HIS229 4.2 47.4 1.0
NH1 D:ARG212 4.2 58.7 1.0
C D:LEU209 4.3 53.4 1.0
CA D:CYS226 4.4 42.5 1.0
N D:HIS229 4.4 42.5 1.0
CA D:CYS207 4.4 53.0 1.0
C D:CYS210 4.7 52.4 1.0
CB D:LEU209 4.7 54.0 1.0
CA D:HIS229 4.7 43.2 1.0
CB D:ARG212 4.7 48.1 1.0
N D:LEU209 4.7 54.2 1.0
CA D:LEU209 4.8 53.7 1.0
O D:LEU209 4.9 54.1 1.0
O D:CYS210 5.0 52.6 1.0
CB D:HIS228 5.0 41.4 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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