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Zinc in PDB 5slx: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z752989138

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z752989138, PDB code: 5slx 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) 69.16 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.044, 68.115, 138.325, 90, 90, 90
R / Rfree (%) 23.6 / 25.9

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 Z752989138 (pdb code 5slx). 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 Z752989138, PDB code: 5slx:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slx

Go back to Zinc Binding Sites List in 5slx
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z752989138


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 Z752989138 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:31.7
occ:1.00
 ND1 D:HIS264 2.1 38.9 1.0
NE2 D:HIS257 2.2 34.3 1.0
SG D:CYS279 2.2 30.4 1.0
SG D:CYS261 2.4 33.9 1.0
CE1 D:HIS264 2.9 39.1 1.0
CD2 D:HIS257 3.1 32.6 1.0
CB D:CYS261 3.1 37.0 1.0
CB D:CYS279 3.1 27.9 1.0
CG D:HIS264 3.2 38.8 1.0
CE1 D:HIS257 3.3 34.2 1.0
CB D:HIS264 3.6 41.5 1.0
NE2 D:HIS264 4.1 39.4 1.0
CG D:HIS257 4.2 32.5 1.0
CD2 D:HIS264 4.2 38.9 1.0
ND1 D:HIS257 4.3 33.5 1.0
N D:HIS264 4.3 43.4 1.0
CA D:CYS261 4.6 38.7 1.0
N D:ASP415 4.6 30.7 1.0
CA D:CYS279 4.6 27.6 1.0
CA D:HIS264 4.6 44.1 1.0
O D:HOH791 4.9 32.1 1.0
SG D:CYS414 4.9 37.2 0.6

Zinc binding site 2 out of 3 in 5slx

Go back to Zinc Binding Sites List in 5slx
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z752989138


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 Z752989138 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:37.0
occ:1.00
 ND1 D:HIS487 2.1 35.6 1.0
SG D:CYS484 2.3 35.4 1.0
SG D:CYS452 2.4 45.0 1.0
SG D:CYS477 2.4 35.4 1.0
CE1 D:HIS487 3.1 36.1 1.0
CG D:HIS487 3.2 34.0 1.0
CB D:CYS452 3.2 43.8 1.0
CB D:CYS477 3.2 34.6 1.0
CB D:CYS484 3.3 35.0 1.0
CB D:HIS487 3.5 32.0 1.0
CA D:CYS452 3.7 44.4 1.0
N D:CYS484 4.0 34.6 1.0
CA D:CYS484 4.2 34.4 1.0
NE2 D:HIS487 4.3 36.0 1.0
CD2 D:HIS487 4.3 35.0 1.0
N D:CYS477 4.4 34.3 1.0
N D:HIS487 4.4 32.0 1.0
CA D:CYS477 4.4 34.6 1.0
CA D:HIS487 4.6 31.8 1.0
N D:CYS452 4.6 43.2 1.0
OG1 D:THR475 4.8 32.7 1.0
CB D:THR475 4.8 31.8 1.0
C D:CYS452 4.9 46.9 1.0
C D:CYS484 4.9 35.0 1.0
O D:CYS484 5.0 34.4 1.0

Zinc binding site 3 out of 3 in 5slx

Go back to Zinc Binding Sites List in 5slx
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z752989138


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 Z752989138 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:43.1
occ:1.00
 ND1 D:HIS229 2.1 44.9 1.0
SG D:CYS207 2.3 45.6 1.0
SG D:CYS210 2.4 48.2 1.0
SG D:CYS226 2.4 39.0 1.0
CE1 D:HIS229 2.9 45.0 1.0
CB D:CYS207 3.1 44.8 1.0
CG D:HIS229 3.2 42.5 1.0
CB D:CYS226 3.4 34.9 1.0
CB D:CYS210 3.4 47.5 1.0
CB D:HIS229 3.7 38.5 1.0
N D:CYS210 3.8 47.8 1.0
N D:CYS226 3.9 34.8 1.0
NE2 D:HIS229 4.1 45.4 1.0
CA D:CYS210 4.1 47.5 1.0
CD2 D:HIS229 4.3 43.9 1.0
CA D:CYS226 4.3 34.3 1.0
NH1 D:ARG212 4.3 45.2 1.0
C D:LEU209 4.4 48.8 1.0
N D:HIS229 4.5 36.6 1.0
CA D:CYS207 4.5 45.3 1.0
C D:CYS210 4.7 47.4 1.0
CD D:ARG212 4.7 44.4 1.0
N D:LEU209 4.7 48.6 1.0
CA D:HIS229 4.8 37.1 1.0
CB D:LEU209 4.8 49.1 1.0
CB D:ARG212 4.8 42.2 1.0
CA D:LEU209 4.9 48.7 1.0
CB D:HIS228 4.9 36.2 1.0
C D:CYS226 5.0 33.1 1.0
O D:CYS210 5.0 47.9 1.0
CG D:ARG212 5.0 43.5 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 07:56:57 2024

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