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Zinc in PDB 5sls: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1373445602

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1373445602, PDB code: 5sls 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) 38.18 / 2.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.508, 67.258, 138.892, 90, 90, 90
R / Rfree (%) 23.6 / 29.3

Other elements in 5sls:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1373445602 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 Z1373445602 (pdb code 5sls). 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 Z1373445602, PDB code: 5sls:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sls

Go back to Zinc Binding Sites List in 5sls
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1373445602


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 Z1373445602 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:71.5
occ:1.00
ND1 D:HIS264 2.0 86.5 1.0
NE2 D:HIS257 2.1 81.9 1.0
SG D:CYS261 2.3 84.5 1.0
SG D:CYS279 2.3 58.7 1.0
CE1 D:HIS264 2.8 86.9 1.0
CB D:CYS261 2.9 81.9 1.0
CE1 D:HIS257 3.0 81.5 1.0
CG D:HIS264 3.1 85.2 1.0
CD2 D:HIS257 3.2 81.1 1.0
CB D:CYS279 3.3 61.2 1.0
CB D:HIS264 3.6 84.7 1.0
NE2 D:HIS264 4.0 86.6 1.0
ND1 D:HIS257 4.1 81.1 1.0
CD2 D:HIS264 4.2 85.8 1.0
N D:HIS264 4.2 84.6 1.0
CG D:HIS257 4.2 79.9 1.0
O D:HOH739 4.3 54.0 1.0
CA D:CYS261 4.4 81.8 1.0
CA D:HIS264 4.5 85.2 1.0
N D:ASP415 4.6 65.5 1.0
O D:CYS261 4.7 81.5 1.0
CA D:CYS279 4.8 62.6 1.0
C D:CYS261 4.8 82.1 1.0
SG D:CYS414 4.8 72.2 0.6
CA D:CYS414 4.9 64.8 0.4
CA D:CYS414 4.9 65.3 0.6

Zinc binding site 2 out of 3 in 5sls

Go back to Zinc Binding Sites List in 5sls
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1373445602


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 Z1373445602 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:80.8
occ:1.00
ND1 D:HIS487 2.2 79.3 1.0
SG D:CYS484 2.4 86.8 1.0
SG D:CYS452 2.4 96.9 1.0
SG D:CYS477 2.5 85.7 1.0
CB D:CYS477 3.2 81.1 1.0
CE1 D:HIS487 3.2 79.4 1.0
CB D:CYS452 3.2 97.3 1.0
CG D:HIS487 3.3 77.6 1.0
CB D:CYS484 3.6 86.5 1.0
CB D:HIS487 3.6 77.3 1.0
CA D:CYS452 3.8 97.9 1.0
N D:CYS484 4.1 86.5 1.0
N D:CYS477 4.3 79.6 1.0
NE2 D:HIS487 4.3 79.3 1.0
CA D:CYS477 4.3 80.0 1.0
CA D:CYS484 4.4 86.5 1.0
CD2 D:HIS487 4.4 78.4 1.0
CB D:THR475 4.5 75.5 1.0
N D:CYS452 4.6 96.0 1.0
OG1 D:THR475 4.6 76.4 1.0
N D:HIS487 4.6 79.2 1.0
CA D:HIS487 4.7 77.7 1.0
CG2 D:THR475 4.9 75.5 1.0

Zinc binding site 3 out of 3 in 5sls

Go back to Zinc Binding Sites List in 5sls
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1373445602


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 Z1373445602 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:93.2
occ:1.00
ND1 D:HIS229 1.9 87.4 1.0
SG D:CYS207 2.2 98.0 1.0
SG D:CYS210 2.3 95.7 1.0
SG D:CYS226 2.4 87.1 1.0
CE1 D:HIS229 2.6 87.8 1.0
CB D:CYS207 2.9 95.8 1.0
CG D:HIS229 3.2 85.2 1.0
CB D:CYS210 3.4 93.6 1.0
CB D:CYS226 3.5 80.8 1.0
N D:CYS210 3.8 93.9 1.0
CB D:HIS229 3.8 81.8 1.0
NH1 D:ARG212 3.8 97.7 1.0
NE2 D:HIS229 3.9 87.4 1.0
N D:CYS226 4.0 79.9 1.0
CA D:CYS210 4.0 93.3 1.0
CD2 D:HIS229 4.1 86.2 1.0
CA D:CYS226 4.3 79.1 1.0
C D:LEU209 4.4 95.0 1.0
CA D:CYS207 4.4 95.5 1.0
C D:CYS210 4.5 92.9 1.0
N D:HIS229 4.6 79.3 1.0
CB D:ARG212 4.7 87.6 1.0
CB D:LEU209 4.7 96.2 1.0
N D:LEU209 4.8 95.9 1.0
O D:CYS210 4.9 93.2 1.0
CA D:HIS229 4.9 80.5 1.0
CA D:LEU209 4.9 95.6 1.0
CG D:ARG212 4.9 89.5 1.0
CD D:ARG212 5.0 91.8 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 07:54:02 2024

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