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Zinc in PDB 5slc: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1849009686

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1849009686, PDB code: 5slc 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) 69.17 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.741, 68.328, 138.333, 90, 90, 90
R / Rfree (%) 24.2 / 26

Other elements in 5slc:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1849009686 also contains other interesting chemical elements:

Fluorine (F) 1 atom

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 Z1849009686 (pdb code 5slc). 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 Z1849009686, PDB code: 5slc:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slc

Go back to Zinc Binding Sites List in 5slc
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1849009686


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 Z1849009686 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:30.7
occ:1.00
ND1 D:HIS264 2.0 35.9 1.0
NE2 D:HIS257 2.2 34.3 1.0
SG D:CYS279 2.2 29.1 1.0
SG D:CYS261 2.4 33.1 1.0
CE1 D:HIS264 2.9 36.1 1.0
CD2 D:HIS257 3.0 32.8 1.0
CB D:CYS279 3.1 26.7 1.0
CB D:CYS261 3.1 36.1 1.0
CG D:HIS264 3.1 35.6 1.0
CE1 D:HIS257 3.2 34.2 1.0
CB D:HIS264 3.6 38.4 1.0
NE2 D:HIS264 4.1 35.9 1.0
CG D:HIS257 4.2 32.6 1.0
CD2 D:HIS264 4.2 35.3 1.0
ND1 D:HIS257 4.3 34.0 1.0
N D:HIS264 4.4 40.4 1.0
N D:ASP415 4.6 28.4 1.0
CA D:CYS279 4.6 25.9 1.0
CA D:CYS261 4.6 37.4 1.0
CA D:HIS264 4.6 40.8 1.0
O D:HOH884 4.8 29.5 1.0
CA D:CYS414 5.0 27.9 0.4
CA D:CYS414 5.0 28.6 0.6
SG D:CYS414 5.0 34.8 0.6

Zinc binding site 2 out of 3 in 5slc

Go back to Zinc Binding Sites List in 5slc
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1849009686


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 Z1849009686 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:32.4
occ:1.00
ND1 D:HIS487 2.1 33.1 1.0
SG D:CYS484 2.3 32.1 1.0
SG D:CYS477 2.3 30.1 1.0
SG D:CYS452 2.4 39.4 1.0
CE1 D:HIS487 3.0 33.0 1.0
CG D:HIS487 3.1 31.1 1.0
CB D:CYS452 3.2 40.6 1.0
CB D:CYS477 3.2 29.5 1.0
CB D:CYS484 3.3 32.1 1.0
CB D:HIS487 3.4 30.6 1.0
CA D:CYS452 3.8 41.9 1.0
N D:CYS484 4.0 31.5 1.0
NE2 D:HIS487 4.2 32.4 1.0
CA D:CYS484 4.2 31.7 1.0
CD2 D:HIS487 4.2 31.8 1.0
N D:CYS477 4.4 30.9 1.0
CA D:CYS477 4.4 29.8 1.0
N D:HIS487 4.4 30.5 1.0
CA D:HIS487 4.5 29.8 1.0
N D:CYS452 4.6 40.5 1.0
OG1 D:THR475 4.6 28.4 1.0
CB D:THR475 4.7 28.3 1.0
C D:CYS484 4.9 32.2 1.0
O D:CYS484 4.9 30.9 1.0
O D:HOH760 5.0 28.5 1.0

Zinc binding site 3 out of 3 in 5slc

Go back to Zinc Binding Sites List in 5slc
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1849009686


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 Z1849009686 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:39.5
occ:1.00
ND1 D:HIS229 2.0 41.3 1.0
SG D:CYS207 2.3 41.5 1.0
SG D:CYS210 2.4 42.8 1.0
SG D:CYS226 2.5 36.3 1.0
CE1 D:HIS229 2.9 41.7 1.0
CB D:CYS207 3.1 40.3 1.0
CG D:HIS229 3.1 39.3 1.0
CB D:CYS210 3.4 42.5 1.0
CB D:CYS226 3.5 33.5 1.0
CB D:HIS229 3.6 36.0 1.0
N D:CYS210 3.7 43.0 1.0
N D:CYS226 4.0 32.7 1.0
CA D:CYS210 4.0 42.5 1.0
NE2 D:HIS229 4.1 42.2 1.0
NH1 D:ARG212 4.2 40.9 1.0
CD2 D:HIS229 4.2 41.0 1.0
C D:LEU209 4.3 44.1 1.0
CA D:CYS226 4.4 32.1 1.0
N D:HIS229 4.4 34.7 1.0
CA D:CYS207 4.5 41.3 1.0
C D:CYS210 4.6 42.8 1.0
CA D:HIS229 4.7 35.2 1.0
N D:LEU209 4.7 43.8 1.0
CB D:LEU209 4.8 44.3 1.0
CA D:LEU209 4.8 43.9 1.0
CB D:ARG212 4.8 38.0 1.0
CD D:ARG212 4.8 39.4 1.0
O D:CYS210 4.9 43.6 1.0
CB D:HIS228 4.9 35.3 1.0
C D:CYS226 5.0 31.4 1.0
O D:LEU209 5.0 45.2 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 07:48:56 2024

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