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Zinc in PDB 5slm: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384, PDB code: 5slm 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) 69.35 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.828, 67.311, 138.691, 90, 90, 90
R / Rfree (%) 25.8 / 30.7

Other elements in 5slm:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384 also contains other interesting chemical elements:

Fluorine (F) 1 atom

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 Z28290384 (pdb code 5slm). 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 Z28290384, PDB code: 5slm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slm

Go back to Zinc Binding Sites List in 5slm
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384


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 Z28290384 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:42.1
occ:1.00
ND1 D:HIS264 2.0 54.2 1.0
NE2 D:HIS257 2.2 50.6 1.0
SG D:CYS279 2.3 40.8 1.0
SG D:CYS261 2.4 49.0 1.0
CE1 D:HIS264 2.9 54.6 1.0
CD2 D:HIS257 3.0 49.3 1.0
CB D:CYS261 3.1 50.0 1.0
CB D:CYS279 3.1 40.0 1.0
CG D:HIS264 3.2 53.5 1.0
CE1 D:HIS257 3.3 50.7 1.0
CB D:HIS264 3.6 54.3 1.0
NE2 D:HIS264 4.1 54.4 1.0
CG D:HIS257 4.2 48.6 1.0
CD2 D:HIS264 4.2 53.7 1.0
ND1 D:HIS257 4.3 50.3 1.0
N D:HIS264 4.4 55.1 1.0
N D:ASP415 4.5 39.8 1.0
CA D:CYS261 4.5 51.0 1.0
CA D:CYS279 4.6 39.9 1.0
CA D:HIS264 4.7 55.8 1.0
O D:HOH727 4.7 48.4 1.0
SG D:CYS414 4.8 42.0 0.6
CA D:CYS414 4.8 39.6 0.4
CA D:CYS414 4.8 39.6 0.6
O D:GLY413 5.0 39.3 1.0

Zinc binding site 2 out of 3 in 5slm

Go back to Zinc Binding Sites List in 5slm
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384


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 Z28290384 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:52.8
occ:1.00
ND1 D:HIS487 2.2 52.0 1.0
SG D:CYS484 2.3 47.3 1.0
SG D:CYS477 2.4 46.5 1.0
SG D:CYS452 2.5 59.5 1.0
CE1 D:HIS487 3.2 52.2 1.0
CB D:CYS477 3.2 43.7 1.0
CG D:HIS487 3.2 49.5 1.0
CB D:CYS484 3.3 47.3 1.0
CB D:CYS452 3.4 63.4 1.0
CB D:HIS487 3.6 47.0 1.0
CA D:CYS452 3.9 65.1 1.0
N D:CYS484 4.1 47.2 1.0
CA D:CYS484 4.3 47.3 1.0
NE2 D:HIS487 4.3 51.9 1.0
CD2 D:HIS487 4.3 50.6 1.0
N D:CYS477 4.3 44.2 1.0
CA D:CYS477 4.4 43.5 1.0
N D:HIS487 4.5 46.4 1.0
CA D:HIS487 4.7 46.1 1.0
CB D:THR475 4.7 45.0 1.0
OG1 D:THR475 4.7 45.2 1.0
N D:CYS452 4.8 63.8 1.0
O D:HOH886 4.9 43.8 1.0
O D:CYS484 4.9 48.4 1.0
C D:CYS484 5.0 48.3 1.0

Zinc binding site 3 out of 3 in 5slm

Go back to Zinc Binding Sites List in 5slm
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384


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 Z28290384 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:52.9
occ:1.00
ND1 D:HIS229 2.0 50.2 1.0
SG D:CYS207 2.3 57.9 1.0
SG D:CYS210 2.5 58.5 1.0
SG D:CYS226 2.5 53.4 1.0
CE1 D:HIS229 2.9 50.9 1.0
CG D:HIS229 3.1 49.0 1.0
CB D:CYS207 3.1 56.5 1.0
CB D:CYS226 3.5 48.8 1.0
CB D:HIS229 3.5 47.8 1.0
CB D:CYS210 3.6 57.8 1.0
N D:CYS210 3.8 57.6 1.0
N D:CYS226 3.9 47.9 1.0
NE2 D:HIS229 4.1 51.1 1.0
CD2 D:HIS229 4.2 50.1 1.0
CA D:CYS210 4.2 57.5 1.0
N D:HIS229 4.3 47.0 1.0
CA D:CYS226 4.3 47.6 1.0
NH1 D:ARG212 4.4 61.2 1.0
C D:LEU209 4.5 58.4 1.0
CA D:HIS229 4.5 47.1 1.0
CA D:CYS207 4.5 56.7 1.0
CB D:LEU209 4.6 58.5 1.0
CB D:ARG212 4.7 54.5 1.0
N D:LEU209 4.8 58.3 1.0
C D:CYS210 4.8 57.8 1.0
CA D:LEU209 4.8 58.4 1.0
CB D:HIS228 4.8 46.8 1.0
C D:CYS226 4.9 46.6 1.0
CD D:ARG212 4.9 58.4 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 07:51:02 2024

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