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Zinc in PDB 5smb: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z419995480

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z419995480, PDB code: 5smb 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) 69.31 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.708, 67.898, 138.629, 90, 90, 90
R / Rfree (%) 23.4 / 28

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 Z419995480 (pdb code 5smb). 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 Z419995480, PDB code: 5smb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5smb

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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 Z419995480


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 Z419995480 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:45.5
occ:1.00
 ND1 D:HIS264 2.0 58.7 1.0
NE2 D:HIS257 2.2 50.1 1.0
SG D:CYS279 2.3 37.2 1.0
SG D:CYS261 2.4 56.6 1.0
CE1 D:HIS264 3.0 59.0 1.0
CD2 D:HIS257 3.1 49.4 1.0
CG D:HIS264 3.1 57.7 1.0
CB D:CYS261 3.1 54.9 1.0
CE1 D:HIS257 3.2 50.2 1.0
CB D:CYS279 3.2 39.6 1.0
CB D:HIS264 3.4 58.3 1.0
NE2 D:HIS264 4.1 59.0 1.0
CD2 D:HIS264 4.2 58.1 1.0
CG D:HIS257 4.2 48.9 1.0
N D:HIS264 4.3 58.8 1.0
ND1 D:HIS257 4.3 50.4 1.0
CA D:HIS264 4.5 59.6 1.0
CA D:CYS261 4.6 54.7 1.0
N D:ASP415 4.6 41.4 1.0
CA D:CYS279 4.7 39.8 1.0
O D:HOH762 4.9 44.6 1.0
CA D:CYS414 4.9 41.5 0.4
C D:CYS261 4.9 55.5 1.0
CA D:CYS414 5.0 41.8 0.6
CA D:MET276 5.0 41.9 1.0

Zinc binding site 2 out of 3 in 5smb

Go back to Zinc Binding Sites List in 5smb
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z419995480


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 Z419995480 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:51.8
occ:1.00
 ND1 D:HIS487 2.2 48.6 1.0
SG D:CYS484 2.2 43.2 1.0
SG D:CYS452 2.4 65.8 1.0
SG D:CYS477 2.4 53.6 1.0
CB D:CYS452 3.1 66.9 1.0
CE1 D:HIS487 3.1 48.6 1.0
CG D:HIS487 3.2 46.6 1.0
CB D:CYS477 3.3 47.9 1.0
CB D:CYS484 3.4 45.9 1.0
CB D:HIS487 3.6 45.1 1.0
CA D:CYS452 3.7 67.6 1.0
N D:CYS484 4.1 47.8 1.0
NE2 D:HIS487 4.2 48.3 1.0
CD2 D:HIS487 4.3 47.3 1.0
CA D:CYS484 4.3 46.9 1.0
N D:CYS477 4.4 47.7 1.0
CA D:CYS477 4.4 47.5 1.0
N D:CYS452 4.5 65.9 1.0
N D:HIS487 4.6 45.2 1.0
CA D:HIS487 4.7 45.3 1.0
CB D:THR475 4.8 47.4 1.0
C D:CYS452 4.8 70.5 1.0
OG1 D:THR475 4.9 47.4 1.0
O D:HOH884 4.9 52.5 1.0
O D:CYS484 5.0 48.5 1.0
C D:CYS484 5.0 48.0 1.0

Zinc binding site 3 out of 3 in 5smb

Go back to Zinc Binding Sites List in 5smb
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z419995480


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 Z419995480 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:59.2
occ:1.00
 ND1 D:HIS229 1.9 57.0 1.0
SG D:CYS207 2.3 66.0 1.0
SG D:CYS210 2.4 62.1 1.0
SG D:CYS226 2.5 55.3 1.0
CE1 D:HIS229 2.8 57.5 1.0
CB D:CYS207 3.0 63.8 1.0
CG D:HIS229 3.1 54.8 1.0
CB D:CYS210 3.5 60.2 1.0
CB D:HIS229 3.6 51.4 1.0
CB D:CYS226 3.6 50.6 1.0
N D:CYS210 3.8 60.3 1.0
NE2 D:HIS229 4.0 57.4 1.0
N D:CYS226 4.0 49.9 1.0
CA D:CYS210 4.1 60.1 1.0
CD2 D:HIS229 4.1 56.1 1.0
C D:LEU209 4.2 61.1 1.0
CA D:CYS226 4.4 49.4 1.0
NH1 D:ARG212 4.4 60.1 1.0
N D:HIS229 4.5 49.9 1.0
CA D:CYS207 4.5 63.7 1.0
CB D:LEU209 4.6 61.7 1.0
N D:LEU209 4.7 62.4 1.0
C D:CYS210 4.7 60.2 1.0
CA D:HIS229 4.7 50.3 1.0
CD D:ARG212 4.7 56.9 1.0
CA D:LEU209 4.7 61.6 1.0
O D:LEU209 4.8 61.5 1.0
CB D:ARG212 4.8 55.4 1.0
CB D:HIS228 4.9 49.7 1.0
O D:CYS210 5.0 60.9 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 08:01:03 2024

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