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Zinc in PDB 5slk: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1354370680

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1354370680, PDB code: 5slk 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) 69.38 / 2.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.596, 67.536, 138.752, 90, 90, 90
R / Rfree (%) 22 / 28.5

Other elements in 5slk:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1354370680 also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 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 Z1354370680 (pdb code 5slk). 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 Z1354370680, PDB code: 5slk:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slk

Go back to Zinc Binding Sites List in 5slk
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1354370680


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 Z1354370680 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:48.1
occ:1.00
 ND1 D:HIS264 1.8 50.6 1.0
NE2 D:HIS257 2.1 56.1 1.0
SG D:CYS261 2.3 54.3 1.0
SG D:CYS279 2.3 36.8 1.0
CE1 D:HIS264 2.7 53.3 1.0
CG D:HIS264 2.9 53.8 1.0
CB D:CYS279 3.0 43.7 1.0
CD2 D:HIS257 3.0 50.1 1.0
CE1 D:HIS257 3.1 49.1 1.0
CB D:CYS261 3.1 58.2 1.0
CB D:HIS264 3.4 56.4 1.0
NE2 D:HIS264 3.9 57.2 1.0
CD2 D:HIS264 4.0 51.7 1.0
CG D:HIS257 4.2 52.8 1.0
ND1 D:HIS257 4.2 48.1 1.0
N D:HIS264 4.2 61.2 1.0
CA D:HIS264 4.4 61.1 1.0
CA D:CYS279 4.5 45.2 1.0
CA D:CYS261 4.6 54.7 1.0
N D:ASP415 4.6 47.3 1.0
O D:HOH707 4.7 45.4 1.0
CA D:MET276 5.0 45.1 1.0
CA D:CYS414 5.0 49.3 0.6
CA D:CYS414 5.0 42.7 0.4

Zinc binding site 2 out of 3 in 5slk

Go back to Zinc Binding Sites List in 5slk
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1354370680


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 Z1354370680 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:52.8
occ:1.00
 SG D:CYS484 2.2 55.5 1.0
ND1 D:HIS487 2.3 47.9 1.0
SG D:CYS477 2.4 59.4 1.0
SG D:CYS452 2.5 63.3 1.0
CB D:CYS452 3.0 64.6 1.0
CB D:CYS477 3.0 57.9 1.0
CB D:CYS484 3.2 55.1 1.0
CE1 D:HIS487 3.2 44.4 1.0
CG D:HIS487 3.3 46.7 1.0
CB D:HIS487 3.5 48.4 1.0
CA D:CYS452 3.6 69.3 1.0
N D:CYS484 3.8 50.8 1.0
CA D:CYS484 4.1 52.2 1.0
CA D:CYS477 4.2 55.7 1.0
N D:CYS477 4.2 55.1 1.0
NE2 D:HIS487 4.3 46.5 1.0
N D:CYS452 4.4 65.5 1.0
CD2 D:HIS487 4.4 46.9 1.0
N D:HIS487 4.6 51.2 1.0
O D:CYS484 4.7 66.8 1.0
CA D:HIS487 4.7 49.9 1.0
CB D:THR475 4.7 54.8 1.0
C D:CYS484 4.7 61.2 1.0
C D:CYS452 4.9 72.3 1.0

Zinc binding site 3 out of 3 in 5slk

Go back to Zinc Binding Sites List in 5slk
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1354370680


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 Z1354370680 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:60.1
occ:1.00
 ND1 D:HIS229 1.9 52.6 1.0
SG D:CYS207 2.2 66.2 1.0
SG D:CYS210 2.4 64.0 1.0
SG D:CYS226 2.5 61.5 1.0
CE1 D:HIS229 2.8 55.3 1.0
CB D:CYS207 2.9 59.4 1.0
CG D:HIS229 3.0 51.7 1.0
CB D:CYS210 3.4 67.5 1.0
CB D:HIS229 3.4 48.3 1.0
CB D:CYS226 3.6 56.0 1.0
N D:CYS210 3.8 63.1 1.0
NE2 D:HIS229 4.0 57.1 1.0
NH1 D:ARG212 4.0 80.1 1.0
N D:CYS226 4.0 52.8 1.0
CD2 D:HIS229 4.1 52.6 1.0
CA D:CYS210 4.1 65.0 1.0
C D:LEU209 4.2 60.1 1.0
CA D:CYS207 4.3 65.2 1.0
CA D:CYS226 4.4 53.9 1.0
N D:HIS229 4.5 56.1 1.0
CB D:LEU209 4.5 60.8 1.0
CA D:HIS229 4.6 49.1 1.0
CB D:ARG212 4.6 67.8 1.0
N D:LEU209 4.7 63.9 1.0
C D:CYS210 4.7 63.4 1.0
CA D:LEU209 4.7 60.5 1.0
O D:LEU209 4.8 62.2 1.0
CB D:HIS228 4.8 51.6 1.0
C D:CYS226 4.9 50.2 1.0
O D:CYS210 4.9 64.3 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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