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Zinc in PDB 5slz: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2072621991

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2072621991, PDB code: 5slz 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) 60.87 / 2.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.7, 67.76, 138.54, 90, 90, 90
R / Rfree (%) 22.2 / 29.4

Other elements in 5slz:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2072621991 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

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 Z2072621991 (pdb code 5slz). 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 Z2072621991, PDB code: 5slz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slz

Go back to Zinc Binding Sites List in 5slz
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2072621991


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 Z2072621991 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:59.8
occ:1.00
ND1 D:HIS264 1.9 68.8 1.0
NE2 D:HIS257 2.2 66.4 1.0
SG D:CYS279 2.3 52.7 1.0
SG D:CYS261 2.4 68.2 1.0
CE1 D:HIS264 2.7 69.4 1.0
CB D:CYS261 2.9 65.9 1.0
CD2 D:HIS257 3.1 65.3 1.0
CG D:HIS264 3.2 67.7 1.0
CB D:CYS279 3.2 53.1 1.0
CE1 D:HIS257 3.3 66.1 1.0
CB D:HIS264 3.7 68.1 1.0
NE2 D:HIS264 3.9 69.4 1.0
CD2 D:HIS264 4.1 68.6 1.0
CG D:HIS257 4.2 64.2 1.0
N D:HIS264 4.3 68.6 1.0
ND1 D:HIS257 4.3 65.7 1.0
CA D:CYS261 4.4 65.8 1.0
N D:ASP415 4.6 52.1 1.0
CA D:HIS264 4.6 69.2 1.0
CA D:CYS279 4.7 53.6 1.0
O D:HOH717 4.7 50.1 1.0
C D:CYS261 4.8 66.7 1.0
O D:CYS261 4.9 66.4 1.0
CA D:CYS414 4.9 52.0 0.4
CA D:CYS414 5.0 52.5 0.6

Zinc binding site 2 out of 3 in 5slz

Go back to Zinc Binding Sites List in 5slz
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2072621991


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 Z2072621991 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:72.5
occ:1.00
ND1 D:HIS487 2.2 65.7 1.0
SG D:CYS484 2.2 68.0 1.0
SG D:CYS452 2.3 79.4 1.0
SG D:CYS477 2.3 65.2 1.0
CB D:CYS452 3.0 80.6 1.0
CE1 D:HIS487 3.2 65.8 1.0
CG D:HIS487 3.2 64.3 1.0
CB D:CYS477 3.4 60.6 1.0
CB D:CYS484 3.5 68.7 1.0
CB D:HIS487 3.5 63.6 1.0
CA D:CYS452 3.6 81.3 1.0
N D:CYS484 4.1 69.6 1.0
NE2 D:HIS487 4.3 65.7 1.0
CD2 D:HIS487 4.3 64.8 1.0
N D:CYS452 4.3 79.9 1.0
CA D:CYS484 4.4 69.0 1.0
N D:HIS487 4.4 63.8 1.0
N D:CYS477 4.5 59.8 1.0
CA D:CYS477 4.5 59.9 1.0
CA D:HIS487 4.6 63.5 1.0
CB D:THR475 4.8 56.9 1.0
C D:CYS452 4.9 83.8 1.0
O D:HOH853 4.9 59.5 1.0

Zinc binding site 3 out of 3 in 5slz

Go back to Zinc Binding Sites List in 5slz
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2072621991


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 Z2072621991 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:71.9
occ:1.00
ND1 D:HIS229 1.9 74.0 1.0
SG D:CYS207 2.2 79.5 1.0
SG D:CYS226 2.5 72.2 1.0
SG D:CYS210 2.5 75.9 1.0
CE1 D:HIS229 2.7 74.6 1.0
CB D:CYS207 2.9 76.5 1.0
CG D:HIS229 3.2 71.7 1.0
CB D:CYS210 3.3 74.4 1.0
CB D:CYS226 3.5 67.1 1.0
CB D:HIS229 3.8 68.4 1.0
N D:CYS210 3.8 73.9 1.0
NE2 D:HIS229 3.9 74.4 1.0
NH1 D:ARG212 3.9 83.2 1.0
N D:CYS226 4.0 66.6 1.0
CA D:CYS210 4.1 74.1 1.0
CD2 D:HIS229 4.1 73.0 1.0
CA D:CYS226 4.3 66.2 1.0
C D:LEU209 4.3 73.8 1.0
CA D:CYS207 4.4 75.9 1.0
N D:HIS229 4.4 67.3 1.0
CB D:LEU209 4.6 74.7 1.0
C D:CYS210 4.7 74.3 1.0
CA D:HIS229 4.8 67.3 1.0
CB D:ARG212 4.8 70.1 1.0
N D:LEU209 4.8 74.5 1.0
CA D:LEU209 4.8 74.3 1.0
CB D:HIS228 4.9 68.2 1.0
O D:LEU209 4.9 73.5 1.0
C D:CYS226 5.0 65.9 1.0
CD D:ARG212 5.0 75.6 1.0
C D:CYS207 5.0 76.8 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: Fri Apr 7 23:31:28 2023

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