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Zinc in PDB 5sl2: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z100643660

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z100643660, PDB code: 5sl2 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) 69.23 / 1.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.977, 67.823, 138.47, 90, 90, 90
R / Rfree (%) 22.6 / 25.6

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 Z100643660 (pdb code 5sl2). 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 Z100643660, PDB code: 5sl2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sl2

Go back to Zinc Binding Sites List in 5sl2
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z100643660


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 Z100643660 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:29.1
occ:1.00
 ND1 D:HIS264 2.0 32.5 1.0
NE2 D:HIS257 2.1 31.4 1.0
SG D:CYS279 2.3 28.3 1.0
SG D:CYS261 2.4 30.0 1.0
CE1 D:HIS264 2.9 32.6 1.0
CD2 D:HIS257 3.0 30.5 1.0
CB D:CYS279 3.1 25.0 1.0
CG D:HIS264 3.1 32.1 1.0
CB D:CYS261 3.2 32.9 1.0
CE1 D:HIS257 3.2 31.1 1.0
CB D:HIS264 3.5 34.4 1.0
NE2 D:HIS264 4.1 32.6 1.0
CG D:HIS257 4.2 30.5 1.0
CD2 D:HIS264 4.2 31.9 1.0
ND1 D:HIS257 4.3 31.0 1.0
N D:HIS264 4.3 36.5 1.0
CA D:HIS264 4.6 37.1 1.0
CA D:CYS279 4.6 25.4 1.0
N D:ASP415 4.6 27.8 1.0
CA D:CYS261 4.6 34.2 1.0
SG D:CYS414 4.9 33.1 0.6
O D:HOH866 5.0 28.1 1.0

Zinc binding site 2 out of 3 in 5sl2

Go back to Zinc Binding Sites List in 5sl2
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z100643660


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 Z100643660 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:32.9
occ:1.00
 ND1 D:HIS487 2.1 31.1 1.0
SG D:CYS477 2.3 29.7 1.0
SG D:CYS484 2.3 31.0 1.0
SG D:CYS452 2.4 40.2 1.0
CE1 D:HIS487 3.0 31.5 1.0
CG D:HIS487 3.1 30.4 1.0
CB D:CYS452 3.2 41.2 1.0
CB D:CYS477 3.2 29.4 1.0
CB D:CYS484 3.3 30.4 1.0
CB D:HIS487 3.5 29.6 1.0
CA D:CYS452 3.8 42.1 1.0
N D:CYS484 4.0 30.5 1.0
CA D:CYS484 4.2 30.3 1.0
NE2 D:HIS487 4.2 31.4 1.0
CD2 D:HIS487 4.3 30.7 1.0
N D:CYS477 4.3 29.6 1.0
CA D:CYS477 4.4 29.6 1.0
N D:HIS487 4.5 29.8 1.0
CA D:HIS487 4.6 29.4 1.0
N D:CYS452 4.6 40.6 1.0
CB D:THR475 4.8 28.1 1.0
OG1 D:THR475 4.8 29.4 1.0
C D:CYS484 4.9 30.5 1.0
O D:CYS484 4.9 28.8 1.0
C D:CYS452 5.0 44.9 1.0

Zinc binding site 3 out of 3 in 5sl2

Go back to Zinc Binding Sites List in 5sl2
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z100643660


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 Z100643660 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:39.1
occ:1.00
 ND1 D:HIS229 1.9 38.7 1.0
SG D:CYS207 2.3 40.0 1.0
SG D:CYS210 2.4 41.5 1.0
SG D:CYS226 2.5 34.8 1.0
CE1 D:HIS229 2.7 39.3 1.0
CB D:CYS207 3.0 38.1 1.0
CG D:HIS229 3.1 36.7 1.0
CB D:CYS210 3.5 41.8 1.0
CB D:CYS226 3.5 31.3 1.0
CB D:HIS229 3.7 34.2 1.0
N D:CYS210 3.8 41.7 1.0
N D:CYS226 3.9 30.8 1.0
NE2 D:HIS229 4.0 39.5 1.0
CA D:CYS210 4.1 41.5 1.0
CD2 D:HIS229 4.2 38.1 1.0
NH1 D:ARG212 4.3 43.7 1.0
CA D:CYS226 4.3 30.6 1.0
C D:LEU209 4.4 42.3 1.0
N D:HIS229 4.5 32.9 1.0
CA D:CYS207 4.5 38.8 1.0
CB D:LEU209 4.7 42.1 1.0
N D:LEU209 4.7 41.8 1.0
C D:CYS210 4.7 42.1 1.0
CA D:HIS229 4.7 33.3 1.0
CB D:ARG212 4.8 38.2 1.0
CA D:LEU209 4.8 42.1 1.0
CD D:ARG212 4.9 40.7 1.0
CB D:HIS228 4.9 32.7 1.0
O D:CYS210 4.9 42.6 1.0
C D:CYS226 5.0 29.5 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 07:45:22 2024

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