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Zinc in PDB 5sm1: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z68277692

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z68277692, PDB code: 5sm1 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) 28.10 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.739, 68.328, 138.512, 90, 90, 90
R / Rfree (%) 22.9 / 26

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 Z68277692 (pdb code 5sm1). 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 Z68277692, PDB code: 5sm1:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sm1

Go back to Zinc Binding Sites List in 5sm1
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z68277692


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 Z68277692 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:35.1
occ:1.00
 ND1 D:HIS264 1.9 42.7 1.0
NE2 D:HIS257 2.1 42.4 1.0
SG D:CYS279 2.3 32.8 1.0
SG D:CYS261 2.4 40.2 1.0
CE1 D:HIS264 2.8 43.1 1.0
CG D:HIS264 3.0 42.0 1.0
CD2 D:HIS257 3.1 41.3 1.0
CB D:CYS279 3.1 30.8 1.0
CB D:CYS261 3.1 41.4 1.0
CE1 D:HIS257 3.2 42.6 1.0
CB D:HIS264 3.5 44.1 1.0
NE2 D:HIS264 4.0 43.0 1.0
CD2 D:HIS264 4.1 41.9 1.0
CG D:HIS257 4.2 40.9 1.0
ND1 D:HIS257 4.2 42.6 1.0
N D:HIS264 4.3 45.8 1.0
CA D:HIS264 4.5 46.4 1.0
N D:ASP415 4.5 34.7 1.0
CA D:CYS279 4.5 31.2 1.0
CA D:CYS261 4.6 42.7 1.0
SG D:CYS414 4.9 39.1 0.6
CA D:CYS414 5.0 34.5 0.4
CA D:CYS414 5.0 35.0 0.6

Zinc binding site 2 out of 3 in 5sm1

Go back to Zinc Binding Sites List in 5sm1
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z68277692


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 Z68277692 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:39.8
occ:1.00
 ND1 D:HIS487 2.2 38.9 1.0
SG D:CYS484 2.2 35.3 1.0
SG D:CYS452 2.3 44.0 1.0
SG D:CYS477 2.4 39.6 1.0
CB D:CYS452 3.2 48.5 1.0
CB D:CYS477 3.2 35.8 1.0
CG D:HIS487 3.2 36.9 1.0
CE1 D:HIS487 3.2 38.9 1.0
CB D:CYS484 3.3 35.9 1.0
CB D:HIS487 3.5 34.9 1.0
CA D:CYS452 3.7 50.3 1.0
N D:CYS484 4.0 36.4 1.0
CA D:CYS484 4.2 36.3 1.0
NE2 D:HIS487 4.4 39.1 1.0
CD2 D:HIS487 4.4 38.0 1.0
CA D:CYS477 4.4 35.9 1.0
N D:CYS477 4.4 36.4 1.0
N D:HIS487 4.4 35.5 1.0
N D:CYS452 4.5 48.6 1.0
CA D:HIS487 4.6 35.1 1.0
CB D:THR475 4.7 36.4 1.0
OG1 D:THR475 4.8 36.9 1.0
O D:CYS484 4.9 37.8 1.0
C D:CYS484 4.9 37.4 1.0
O D:HOH834 4.9 35.3 1.0
C D:CYS452 5.0 54.0 1.0

Zinc binding site 3 out of 3 in 5sm1

Go back to Zinc Binding Sites List in 5sm1
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z68277692


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 Z68277692 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:46.8
occ:1.00
 ND1 D:HIS229 1.9 45.7 1.0
SG D:CYS207 2.4 50.8 1.0
SG D:CYS210 2.4 51.0 1.0
SG D:CYS226 2.5 44.9 1.0
CE1 D:HIS229 2.8 46.4 1.0
CB D:CYS207 3.1 50.2 1.0
CG D:HIS229 3.1 43.8 1.0
CB D:CYS210 3.5 50.3 1.0
CB D:CYS226 3.5 39.7 1.0
CB D:HIS229 3.6 40.8 1.0
N D:CYS210 3.8 50.8 1.0
NE2 D:HIS229 4.0 46.4 1.0
N D:CYS226 4.0 39.4 1.0
CA D:CYS210 4.1 50.3 1.0
CD2 D:HIS229 4.1 45.2 1.0
NH1 D:ARG212 4.2 50.6 1.0
CA D:CYS226 4.3 38.6 1.0
C D:LEU209 4.4 52.0 1.0
N D:HIS229 4.4 39.2 1.0
CA D:CYS207 4.6 50.7 1.0
CB D:LEU209 4.6 52.6 1.0
CA D:HIS229 4.7 39.4 1.0
C D:CYS210 4.7 50.4 1.0
N D:LEU209 4.7 52.4 1.0
CD D:ARG212 4.7 46.8 1.0
CB D:ARG212 4.8 45.5 1.0
CA D:LEU209 4.8 52.3 1.0
CB D:HIS228 4.8 38.7 1.0
O D:CYS210 4.9 50.9 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 07:56:57 2024

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