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Zinc in PDB 5smg: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2092370954

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2092370954, PDB code: 5smg 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) 69.27 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.422, 68.042, 138.544, 90, 90, 90
R / Rfree (%) 23.1 / 25.3

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 Z2092370954 (pdb code 5smg). 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 Z2092370954, PDB code: 5smg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5smg

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Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2092370954


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 Z2092370954 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:36.4
occ:1.00
 ND1 D:HIS264 2.0 40.7 1.0
NE2 D:HIS257 2.1 40.9 1.0
SG D:CYS279 2.3 35.2 1.0
SG D:CYS261 2.4 40.1 1.0
CE1 D:HIS264 2.8 41.2 1.0
CD2 D:HIS257 2.9 40.4 1.0
CG D:HIS264 3.1 40.8 1.0
CB D:CYS279 3.1 32.0 1.0
CB D:CYS261 3.2 40.4 1.0
CE1 D:HIS257 3.2 41.2 1.0
CB D:HIS264 3.6 44.2 1.0
NE2 D:HIS264 4.0 41.3 1.0
CG D:HIS257 4.1 39.9 1.0
CD2 D:HIS264 4.2 40.4 1.0
ND1 D:HIS257 4.3 41.0 1.0
N D:HIS264 4.3 47.3 1.0
N D:ASP415 4.6 35.6 1.0
CA D:HIS264 4.6 47.3 1.0
CA D:CYS279 4.6 31.7 1.0
CA D:CYS261 4.6 41.6 1.0
CA D:CYS414 4.9 35.3 0.4
CA D:CYS414 5.0 35.2 0.6
O D:HOH808 5.0 36.5 1.0
SG D:CYS414 5.0 38.1 0.6

Zinc binding site 2 out of 3 in 5smg

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Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2092370954


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 Z2092370954 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:42.0
occ:1.00
 ND1 D:HIS487 2.1 37.7 1.0
SG D:CYS452 2.2 48.0 1.0
SG D:CYS484 2.3 42.1 1.0
SG D:CYS477 2.4 40.9 1.0
CE1 D:HIS487 3.1 37.5 1.0
CG D:HIS487 3.1 35.8 1.0
CB D:CYS452 3.2 53.0 1.0
CB D:CYS477 3.2 38.3 1.0
CB D:CYS484 3.3 41.0 1.0
CB D:HIS487 3.4 35.0 1.0
CA D:CYS452 3.7 54.9 1.0
N D:CYS484 4.0 40.4 1.0
CA D:CYS484 4.2 40.7 1.0
NE2 D:HIS487 4.2 37.2 1.0
CD2 D:HIS487 4.2 36.6 1.0
N D:CYS477 4.3 39.0 1.0
CA D:CYS477 4.4 38.5 1.0
N D:HIS487 4.4 36.5 1.0
CA D:HIS487 4.5 35.8 1.0
N D:CYS452 4.6 53.3 1.0
OG1 D:THR475 4.6 36.8 1.0
CB D:THR475 4.7 36.3 1.0
C D:CYS484 4.9 41.1 1.0
O D:CYS484 4.9 41.2 1.0
C D:CYS452 5.0 58.3 1.0

Zinc binding site 3 out of 3 in 5smg

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Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2092370954


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 Z2092370954 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:48.2
occ:1.00
 ND1 D:HIS229 2.0 48.1 1.0
SG D:CYS207 2.3 51.9 1.0
SG D:CYS210 2.3 53.6 1.0
SG D:CYS226 2.4 44.4 1.0
CE1 D:HIS229 2.8 48.7 1.0
CB D:CYS207 3.0 51.0 1.0
CG D:HIS229 3.2 46.0 1.0
CB D:CYS210 3.4 53.1 1.0
CB D:CYS226 3.5 40.2 1.0
CB D:HIS229 3.7 42.4 1.0
N D:CYS210 3.8 53.8 1.0
N D:CYS226 3.9 39.9 1.0
NE2 D:HIS229 4.0 48.8 1.0
CA D:CYS210 4.1 53.2 1.0
CD2 D:HIS229 4.2 47.5 1.0
NH1 D:ARG212 4.2 51.5 1.0
CA D:CYS226 4.3 39.5 1.0
C D:LEU209 4.3 54.7 1.0
N D:HIS229 4.4 40.4 1.0
CA D:CYS207 4.5 51.4 1.0
CB D:LEU209 4.7 55.2 1.0
C D:CYS210 4.7 53.6 1.0
CD D:ARG212 4.7 48.9 1.0
CA D:HIS229 4.7 41.1 1.0
CB D:ARG212 4.8 47.1 1.0
N D:LEU209 4.8 54.9 1.0
CA D:LEU209 4.8 54.8 1.0
O D:CYS210 4.9 54.1 1.0
CB D:HIS228 4.9 40.3 1.0
O D:LEU209 5.0 55.2 1.0
C D:CYS226 5.0 38.4 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 08:02:58 2024

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