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Zinc in PDB 5sle: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56880342

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56880342, PDB code: 5sle 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) 61.32 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.651, 68.431, 138.191, 90, 90, 90
R / Rfree (%) 22.6 / 26.1

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 Z56880342 (pdb code 5sle). 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 Z56880342, PDB code: 5sle:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sle

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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 Z56880342


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 Z56880342 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:37.6
occ:1.00
 ND1 D:HIS264 2.0 47.7 1.0
NE2 D:HIS257 2.1 42.1 1.0
SG D:CYS279 2.3 34.3 1.0
SG D:CYS261 2.4 44.0 1.0
CE1 D:HIS264 2.9 48.1 1.0
CD2 D:HIS257 3.0 41.3 1.0
CG D:HIS264 3.1 46.8 1.0
CB D:CYS261 3.1 44.2 1.0
CB D:CYS279 3.1 33.8 1.0
CE1 D:HIS257 3.2 42.3 1.0
CB D:HIS264 3.5 48.2 1.0
NE2 D:HIS264 4.1 48.1 1.0
CG D:HIS257 4.2 41.0 1.0
CD2 D:HIS264 4.2 46.9 1.0
N D:HIS264 4.3 49.4 1.0
ND1 D:HIS257 4.3 42.5 1.0
CA D:HIS264 4.5 50.1 1.0
CA D:CYS261 4.5 44.9 1.0
N D:ASP415 4.6 36.8 1.0
CA D:CYS279 4.6 34.2 1.0
O D:HOH728 4.9 37.1 1.0
SG D:CYS414 4.9 37.9 0.6
C D:CYS261 5.0 45.5 1.0
CA D:CYS414 5.0 36.5 0.4
CA D:CYS414 5.0 36.5 0.6

Zinc binding site 2 out of 3 in 5sle

Go back to Zinc Binding Sites List in 5sle
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56880342


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 Z56880342 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:43.0
occ:1.00
 ND1 D:HIS487 2.1 40.7 1.0
SG D:CYS484 2.2 41.7 1.0
SG D:CYS452 2.3 50.4 1.0
SG D:CYS477 2.4 41.8 1.0
CE1 D:HIS487 3.1 40.8 1.0
CG D:HIS487 3.2 39.2 1.0
CB D:CYS477 3.2 39.5 1.0
CB D:CYS452 3.3 53.6 1.0
CB D:CYS484 3.3 39.8 1.0
CB D:HIS487 3.5 37.7 1.0
CA D:CYS452 3.8 55.0 1.0
N D:CYS484 4.0 39.1 1.0
CA D:CYS484 4.2 39.3 1.0
NE2 D:HIS487 4.2 40.6 1.0
CD2 D:HIS487 4.3 39.5 1.0
N D:CYS477 4.3 39.4 1.0
CA D:CYS477 4.4 39.3 1.0
N D:HIS487 4.5 38.3 1.0
N D:CYS452 4.6 53.3 1.0
CA D:HIS487 4.6 38.3 1.0
CB D:THR475 4.7 36.8 1.0
OG1 D:THR475 4.7 37.6 1.0
C D:CYS484 4.9 39.9 1.0
O D:HOH777 4.9 37.2 1.0
O D:CYS484 4.9 40.4 1.0

Zinc binding site 3 out of 3 in 5sle

Go back to Zinc Binding Sites List in 5sle
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56880342


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 Z56880342 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:48.7
occ:1.00
 ND1 D:HIS229 2.0 46.2 1.0
SG D:CYS210 2.3 52.1 1.0
SG D:CYS207 2.4 49.4 1.0
SG D:CYS226 2.5 45.2 1.0
CE1 D:HIS229 2.8 46.9 1.0
CB D:CYS207 3.1 49.1 1.0
CG D:HIS229 3.2 44.6 1.0
CB D:CYS210 3.5 50.1 1.0
CB D:CYS226 3.5 41.5 1.0
CB D:HIS229 3.7 42.2 1.0
N D:CYS210 3.9 49.9 1.0
N D:CYS226 4.0 41.2 1.0
NE2 D:HIS229 4.0 47.3 1.0
NH1 D:ARG212 4.1 50.4 1.0
CA D:CYS210 4.1 49.8 1.0
CD2 D:HIS229 4.2 46.1 1.0
CA D:CYS226 4.4 40.6 1.0
C D:LEU209 4.4 50.9 1.0
N D:HIS229 4.5 40.7 1.0
CA D:CYS207 4.6 49.4 1.0
C D:CYS210 4.7 50.5 1.0
CB D:LEU209 4.7 51.1 1.0
CB D:ARG212 4.7 46.1 1.0
CA D:HIS229 4.8 41.3 1.0
N D:LEU209 4.8 51.4 1.0
CD D:ARG212 4.8 47.4 1.0
CB D:HIS228 4.8 39.9 1.0
CA D:LEU209 4.8 51.0 1.0
O D:CYS210 4.9 51.3 1.0
O D:LEU209 4.9 51.7 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 07:48:56 2024

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