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Zinc in PDB 5slj: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1430613393

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1430613393, PDB code: 5slj 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) 69.28 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.183, 67.638, 138.562, 90, 90, 90
R / Rfree (%) 18.1 / 24.7

Other elements in 5slj:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1430613393 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 Z1430613393 (pdb code 5slj). 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 Z1430613393, PDB code: 5slj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slj

Go back to Zinc Binding Sites List in 5slj
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1430613393


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 Z1430613393 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:32.4
occ:1.00
ND1 D:HIS264 1.9 31.6 1.0
NE2 D:HIS257 2.1 38.5 1.0
SG D:CYS279 2.2 30.1 1.0
SG D:CYS261 2.4 35.0 1.0
CE1 D:HIS264 2.8 35.8 1.0
CD2 D:HIS257 3.0 34.0 1.0
CB D:CYS279 3.0 31.9 1.0
CG D:HIS264 3.1 38.0 1.0
CE1 D:HIS257 3.1 34.6 1.0
CB D:CYS261 3.1 37.6 1.0
CB D:HIS264 3.5 39.2 1.0
NE2 D:HIS264 4.0 32.9 1.0
CD2 D:HIS264 4.1 33.3 1.0
ND1 D:HIS257 4.2 34.2 1.0
CG D:HIS257 4.2 35.4 1.0
N D:HIS264 4.3 38.3 1.0
N D:ASP415 4.5 34.5 1.0
CA D:CYS279 4.5 30.8 1.0
CA D:HIS264 4.6 39.4 1.0
CA D:CYS261 4.6 39.0 1.0
CA D:CYS414 4.9 33.5 0.6
CA D:CYS414 5.0 31.3 0.4
C D:CYS261 5.0 38.6 1.0

Zinc binding site 2 out of 3 in 5slj

Go back to Zinc Binding Sites List in 5slj
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1430613393


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 Z1430613393 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:36.0
occ:1.00
ND1 D:HIS487 2.2 28.9 1.0
SG D:CYS484 2.2 32.9 1.0
SG D:CYS477 2.3 33.4 1.0
SG D:CYS452 2.4 44.1 1.0
CG D:HIS487 3.1 30.6 1.0
CE1 D:HIS487 3.1 29.5 1.0
CB D:CYS452 3.2 46.4 1.0
CB D:CYS477 3.2 32.7 1.0
CB D:CYS484 3.3 35.3 1.0
CB D:HIS487 3.4 30.4 1.0
CA D:CYS452 3.8 49.4 1.0
N D:CYS484 3.9 34.0 1.0
CA D:CYS484 4.1 33.9 1.0
NE2 D:HIS487 4.3 28.2 1.0
CD2 D:HIS487 4.3 28.9 1.0
N D:CYS477 4.3 34.9 1.0
CA D:CYS477 4.4 31.4 1.0
N D:HIS487 4.5 35.4 1.0
N D:CYS452 4.6 42.9 1.0
CA D:HIS487 4.6 33.8 1.0
CB D:THR475 4.7 32.0 1.0
OG1 D:THR475 4.7 35.0 1.0
C D:CYS484 4.8 38.8 1.0
O D:CYS484 4.9 40.2 1.0
O D:HOH849 4.9 26.4 1.0
C D:CYS452 5.0 49.2 1.0

Zinc binding site 3 out of 3 in 5slj

Go back to Zinc Binding Sites List in 5slj
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1430613393


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 Z1430613393 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:40.3
occ:1.00
ND1 D:HIS229 2.0 35.1 1.0
SG D:CYS207 2.4 45.3 1.0
SG D:CYS210 2.4 45.5 1.0
SG D:CYS226 2.5 39.9 1.0
CB D:CYS207 2.8 39.0 1.0
CE1 D:HIS229 2.9 40.8 1.0
CG D:HIS229 3.0 36.1 1.0
CB D:CYS210 3.4 47.6 1.0
CB D:HIS229 3.4 36.8 1.0
CB D:CYS226 3.6 40.2 1.0
N D:CYS210 3.7 43.6 1.0
N D:CYS226 4.0 35.5 1.0
CA D:CYS210 4.0 43.5 1.0
NE2 D:HIS229 4.1 35.2 1.0
CD2 D:HIS229 4.1 38.8 1.0
NH1 D:ARG212 4.2 49.5 1.0
CA D:CYS207 4.3 45.5 1.0
C D:LEU209 4.4 48.9 1.0
CA D:CYS226 4.4 35.4 1.0
N D:HIS229 4.5 41.0 1.0
CB D:LEU209 4.6 44.9 1.0
CA D:HIS229 4.6 38.2 1.0
C D:CYS210 4.6 45.0 1.0
N D:LEU209 4.7 48.0 1.0
CB D:ARG212 4.8 46.2 1.0
CB D:HIS228 4.8 36.9 1.0
CA D:LEU209 4.8 48.0 1.0
C D:CYS226 5.0 35.5 1.0
O D:CYS210 5.0 47.7 1.0
C D:CYS207 5.0 44.5 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: Fri Apr 7 23:24:27 2023

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