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Zinc in PDB 5slv: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942, PDB code: 5slv 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) 29.82 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.621, 68.456, 138.65, 90, 90, 90
R / Rfree (%) 24.4 / 28

Other elements in 5slv:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942 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 Z2856434942 (pdb code 5slv). 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 Z2856434942, PDB code: 5slv:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slv

Go back to Zinc Binding Sites List in 5slv
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:45.3
occ:1.00
ND1 D:HIS264 1.9 49.0 1.0
NE2 D:HIS257 2.1 50.6 1.0
SG D:CYS279 2.2 41.6 1.0
SG D:CYS261 2.4 56.2 1.0
CE1 D:HIS264 2.8 49.3 1.0
CD2 D:HIS257 3.0 50.0 1.0
CG D:HIS264 3.1 48.8 1.0
CB D:CYS261 3.1 55.7 1.0
CB D:CYS279 3.1 40.9 1.0
CE1 D:HIS257 3.1 50.7 1.0
CB D:HIS264 3.5 52.0 1.0
NE2 D:HIS264 4.0 49.0 1.0
CG D:HIS257 4.1 49.6 1.0
CD2 D:HIS264 4.1 48.5 1.0
ND1 D:HIS257 4.2 51.0 1.0
N D:HIS264 4.3 55.5 1.0
N D:ASP415 4.5 43.5 1.0
CA D:CYS261 4.6 56.3 1.0
CA D:HIS264 4.6 55.2 1.0
CA D:CYS279 4.6 41.0 1.0
CA D:CYS414 4.9 42.3 0.4
CA D:CYS414 4.9 43.0 0.6
SG D:CYS414 4.9 47.9 0.6
C D:CYS261 5.0 56.5 1.0

Zinc binding site 2 out of 3 in 5slv

Go back to Zinc Binding Sites List in 5slv
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:51.8
occ:1.00
SG D:CYS484 2.2 48.3 1.0
ND1 D:HIS487 2.2 50.6 1.0
SG D:CYS452 2.3 59.8 1.0
SG D:CYS477 2.5 55.6 1.0
CB D:CYS477 3.2 49.4 1.0
CE1 D:HIS487 3.2 50.4 1.0
CG D:HIS487 3.2 48.7 1.0
CB D:CYS452 3.3 63.4 1.0
CB D:CYS484 3.3 50.7 1.0
CB D:HIS487 3.5 47.3 1.0
CA D:CYS452 3.8 64.9 1.0
N D:CYS484 4.0 51.5 1.0
CA D:CYS484 4.2 51.2 1.0
NE2 D:HIS487 4.4 50.4 1.0
N D:CYS477 4.4 48.8 1.0
CD2 D:HIS487 4.4 49.6 1.0
CA D:CYS477 4.4 48.5 1.0
N D:HIS487 4.5 47.8 1.0
N D:CYS452 4.6 63.4 1.0
CA D:HIS487 4.6 47.5 1.0
CB D:THR475 4.8 46.9 1.0
O D:CYS484 4.9 51.9 1.0
C D:CYS484 4.9 51.6 1.0
O D:HOH844 4.9 52.5 1.0
OG1 D:THR475 4.9 47.2 1.0

Zinc binding site 3 out of 3 in 5slv

Go back to Zinc Binding Sites List in 5slv
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:58.9
occ:1.00
ND1 D:HIS229 2.0 56.6 1.0
SG D:CYS210 2.3 66.8 1.0
SG D:CYS207 2.4 60.4 1.0
SG D:CYS226 2.4 57.7 1.0
CE1 D:HIS229 2.8 57.0 1.0
CB D:CYS207 3.1 62.0 1.0
CG D:HIS229 3.2 54.6 1.0
CB D:CYS210 3.4 63.9 1.0
CB D:CYS226 3.5 51.2 1.0
CB D:HIS229 3.7 52.2 1.0
N D:CYS210 3.8 63.0 1.0
N D:CYS226 4.0 49.7 1.0
NE2 D:HIS229 4.0 57.3 1.0
CA D:CYS210 4.1 63.2 1.0
CD2 D:HIS229 4.2 56.0 1.0
CA D:CYS226 4.3 49.3 1.0
NH1 D:ARG212 4.3 63.9 1.0
C D:LEU209 4.4 63.6 1.0
N D:HIS229 4.5 50.9 1.0
CA D:CYS207 4.6 62.9 1.0
CB D:LEU209 4.7 63.9 1.0
C D:CYS210 4.7 63.5 1.0
CD D:ARG212 4.8 59.8 1.0
CB D:ARG212 4.8 58.1 1.0
CA D:HIS229 4.8 51.3 1.0
N D:LEU209 4.8 63.9 1.0
CA D:LEU209 4.8 63.7 1.0
CB D:HIS228 5.0 50.0 1.0
C D:CYS226 5.0 48.3 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 07:54:02 2024

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