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Zinc in PDB 5sln: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57299529

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57299529, PDB code: 5sln 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) 28.05 / 2.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.499, 67.636, 138.588, 90, 90, 90
R / Rfree (%) 24 / 29.8

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 Z57299529 (pdb code 5sln). 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 Z57299529, PDB code: 5sln:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sln

Go back to Zinc Binding Sites List in 5sln
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57299529


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 Z57299529 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:54.1
occ:1.00
 ND1 D:HIS264 2.1 64.2 1.0
NE2 D:HIS257 2.2 61.3 1.0
SG D:CYS279 2.3 46.4 1.0
SG D:CYS261 2.4 61.7 1.0
CE1 D:HIS264 3.1 64.3 1.0
CB D:CYS261 3.1 62.8 1.0
CG D:HIS264 3.1 63.0 1.0
CE1 D:HIS257 3.1 61.2 1.0
CB D:CYS279 3.2 46.8 1.0
CD2 D:HIS257 3.2 60.4 1.0
CB D:HIS264 3.4 63.7 1.0
NE2 D:HIS264 4.2 64.2 1.0
CD2 D:HIS264 4.2 63.4 1.0
N D:HIS264 4.3 64.2 1.0
ND1 D:HIS257 4.3 61.0 1.0
CG D:HIS257 4.3 59.5 1.0
CA D:HIS264 4.5 64.9 1.0
CA D:CYS261 4.5 63.6 1.0
N D:ASP415 4.6 47.9 1.0
CA D:CYS279 4.6 46.9 1.0
SG D:CYS414 4.8 55.0 0.6
CA D:CYS414 4.9 46.5 0.4
CA D:CYS414 4.9 47.8 0.6
C D:CYS261 5.0 64.0 1.0

Zinc binding site 2 out of 3 in 5sln

Go back to Zinc Binding Sites List in 5sln
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57299529


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 Z57299529 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:59.0
occ:1.00
 SG D:CYS484 2.2 57.7 1.0
ND1 D:HIS487 2.3 57.9 1.0
SG D:CYS452 2.4 76.1 1.0
SG D:CYS477 2.4 62.8 1.0
CB D:CYS477 3.1 57.0 1.0
CB D:CYS452 3.2 74.4 1.0
CG D:HIS487 3.3 55.9 1.0
CE1 D:HIS487 3.3 57.7 1.0
CB D:CYS484 3.4 57.4 1.0
CB D:HIS487 3.5 54.7 1.0
CA D:CYS452 3.9 74.3 1.0
N D:CYS484 3.9 56.9 1.0
CA D:CYS484 4.2 57.2 1.0
CA D:CYS477 4.3 56.1 1.0
N D:CYS477 4.3 55.9 1.0
NE2 D:HIS487 4.5 57.8 1.0
CD2 D:HIS487 4.5 56.8 1.0
N D:HIS487 4.5 54.5 1.0
CA D:HIS487 4.6 54.4 1.0
N D:CYS452 4.7 73.0 1.0
CB D:THR475 4.7 55.0 1.0
OG1 D:THR475 4.8 56.1 1.0
O D:HOH896 4.8 52.3 1.0
O D:CYS484 4.8 58.7 1.0
C D:CYS484 4.9 57.9 1.0

Zinc binding site 3 out of 3 in 5sln

Go back to Zinc Binding Sites List in 5sln
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z57299529


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 Z57299529 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:66.1
occ:1.00
 ND1 D:HIS229 1.9 59.5 1.0
SG D:CYS210 2.2 71.8 1.0
SG D:CYS207 2.3 71.3 1.0
SG D:CYS226 2.5 62.0 1.0
CE1 D:HIS229 2.6 60.1 1.0
CB D:CYS207 2.9 69.5 1.0
CG D:HIS229 3.2 57.5 1.0
CB D:CYS226 3.4 57.5 1.0
CB D:CYS210 3.5 69.3 1.0
CB D:HIS229 3.8 55.6 1.0
NE2 D:HIS229 3.9 59.9 1.0
N D:CYS210 3.9 68.7 1.0
N D:CYS226 4.0 56.4 1.0
CA D:CYS210 4.1 68.4 1.0
CD2 D:HIS229 4.1 58.8 1.0
C D:LEU209 4.3 70.0 1.0
CA D:CYS226 4.3 56.4 1.0
NH1 D:ARG212 4.4 70.5 1.0
CA D:CYS207 4.4 69.2 1.0
N D:HIS229 4.5 55.5 1.0
CB D:ARG212 4.6 63.5 1.0
CB D:LEU209 4.7 70.5 1.0
C D:CYS210 4.7 68.2 1.0
CD D:ARG212 4.7 66.9 1.0
N D:LEU209 4.8 70.5 1.0
O D:LEU209 4.8 71.0 1.0
CA D:LEU209 4.8 70.2 1.0
CA D:HIS229 4.8 55.4 1.0
CG D:ARG212 4.9 64.8 1.0
CB D:HIS228 5.0 56.4 1.0
O D:CYS210 5.0 68.4 1.0
C D:CYS207 5.0 70.5 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: Mon Oct 28 07:51:02 2024

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