Zinc in PDB 5slh: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z65532537

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z65532537, PDB code: 5slh 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) 69.29 / 1.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.502, 67.783, 138.589, 90, 90, 90
R / Rfree (%) 23.8 / 26.4

Other elements in 5slh:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z65532537 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 Z65532537 (pdb code 5slh). 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 Z65532537, PDB code: 5slh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slh

Go back to Zinc Binding Sites List in 5slh
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z65532537


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 Z65532537 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:36.3
occ:1.00
 ND1 D:HIS264 2.0 39.7 1.0
NE2 D:HIS257 2.1 38.5 1.0
SG D:CYS279 2.2 32.5 1.0
SG D:CYS261 2.4 39.0 1.0
CD2 D:HIS257 3.0 37.8 1.0
CE1 D:HIS264 3.0 39.9 1.0
CB D:CYS279 3.1 29.2 1.0
CG D:HIS264 3.1 39.9 1.0
CB D:CYS261 3.2 40.9 1.0
CE1 D:HIS257 3.2 38.2 1.0
CB D:HIS264 3.5 44.2 1.0
NE2 D:HIS264 4.1 40.5 1.0
CG D:HIS257 4.1 37.4 1.0
CD2 D:HIS264 4.2 39.7 1.0
ND1 D:HIS257 4.3 38.4 1.0
N D:HIS264 4.3 47.0 1.0
CA D:HIS264 4.5 47.1 1.0
CA D:CYS279 4.6 29.2 1.0
N D:ASP415 4.6 34.8 1.0
CA D:CYS261 4.6 42.5 1.0
O D:HOH761 4.9 29.9 1.0
SG D:CYS414 4.9 39.1 0.6
CA D:CYS414 5.0 34.9 0.4
CA D:CYS414 5.0 35.1 0.6

Zinc binding site 2 out of 3 in 5slh

Go back to Zinc Binding Sites List in 5slh
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z65532537


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 Z65532537 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:40.3
occ:1.00
 ND1 D:HIS487 2.1 39.0 1.0
SG D:CYS484 2.3 38.2 1.0
SG D:CYS452 2.3 50.7 1.0
SG D:CYS477 2.4 38.6 1.0
CE1 D:HIS487 3.1 38.7 1.0
CG D:HIS487 3.1 37.0 1.0
CB D:CYS477 3.1 36.5 1.0
CB D:CYS452 3.2 53.6 1.0
CB D:CYS484 3.2 39.0 1.0
CB D:HIS487 3.4 36.0 1.0
CA D:CYS452 3.8 54.9 1.0
N D:CYS484 4.0 38.5 1.0
CA D:CYS484 4.2 39.0 1.0
NE2 D:HIS487 4.2 38.3 1.0
CD2 D:HIS487 4.3 37.6 1.0
CA D:CYS477 4.3 36.4 1.0
N D:CYS477 4.3 37.4 1.0
N D:HIS487 4.5 37.4 1.0
CA D:HIS487 4.6 36.8 1.0
N D:CYS452 4.6 52.9 1.0
OG1 D:THR475 4.6 36.8 1.0
CB D:THR475 4.7 35.5 1.0
C D:CYS484 4.8 40.2 1.0
O D:CYS484 4.9 40.2 1.0

Zinc binding site 3 out of 3 in 5slh

Go back to Zinc Binding Sites List in 5slh
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z65532537


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 Z65532537 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:47.6
occ:1.00
 ND1 D:HIS229 1.9 45.5 1.0
SG D:CYS207 2.3 52.9 1.0
SG D:CYS210 2.4 52.5 1.0
SG D:CYS226 2.4 45.4 1.0
CE1 D:HIS229 2.7 45.7 1.0
CB D:CYS207 3.1 50.1 1.0
CG D:HIS229 3.1 43.6 1.0
CB D:CYS210 3.4 51.7 1.0
CB D:CYS226 3.5 40.3 1.0
CB D:HIS229 3.7 41.0 1.0
N D:CYS210 3.8 52.0 1.0
N D:CYS226 3.9 39.7 1.0
NE2 D:HIS229 4.0 46.3 1.0
CA D:CYS210 4.1 51.7 1.0
CD2 D:HIS229 4.2 45.3 1.0
NH1 D:ARG212 4.2 51.9 1.0
CA D:CYS226 4.3 39.3 1.0
C D:LEU209 4.4 52.7 1.0
N D:HIS229 4.5 39.9 1.0
CA D:CYS207 4.5 50.1 1.0
C D:CYS210 4.6 51.9 1.0
CD D:ARG212 4.7 49.6 1.0
CB D:LEU209 4.7 53.0 1.0
CA D:HIS229 4.8 40.5 1.0
CB D:ARG212 4.8 47.3 1.0
N D:LEU209 4.8 52.4 1.0
CA D:LEU209 4.8 52.6 1.0
O D:CYS210 4.9 52.7 1.0
CB D:HIS228 5.0 39.3 1.0
C D:CYS226 5.0 38.1 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 07:51:02 2024

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