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Zinc in PDB 5smf: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867, PDB code: 5smf 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) 69.30 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.145, 67.846, 138.596, 90, 90, 90
R / Rfree (%) 27 / 31.9

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 Z56791867 (pdb code 5smf). 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 Z56791867, PDB code: 5smf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5smf

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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 Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:52.7
occ:1.00
 ND1 D:HIS264 2.1 61.5 1.0
NE2 D:HIS257 2.1 59.5 1.0
SG D:CYS279 2.3 49.6 1.0
SG D:CYS261 2.4 58.3 1.0
CE1 D:HIS264 3.0 61.6 1.0
CB D:CYS261 3.0 58.3 1.0
CD2 D:HIS257 3.1 58.0 1.0
CE1 D:HIS257 3.1 59.3 1.0
CG D:HIS264 3.1 60.7 1.0
CB D:CYS279 3.2 47.2 1.0
CB D:HIS264 3.5 62.3 1.0
NE2 D:HIS264 4.1 61.1 1.0
CG D:HIS257 4.1 57.2 1.0
ND1 D:HIS257 4.1 58.9 1.0
CD2 D:HIS264 4.2 60.4 1.0
N D:HIS264 4.3 63.7 1.0
CA D:CYS261 4.5 59.2 1.0
N D:ASP415 4.5 51.5 1.0
CA D:HIS264 4.5 64.1 1.0
CA D:CYS279 4.6 47.3 1.0
O D:HOH756 4.8 59.9 1.0
CA D:CYS414 4.8 49.7 0.4
SG D:CYS414 4.9 52.2 0.6
CA D:CYS414 4.9 50.0 0.6
C D:CYS261 4.9 59.6 1.0

Zinc binding site 2 out of 3 in 5smf

Go back to Zinc Binding Sites List in 5smf
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:59.5
occ:1.00
 SG D:CYS484 2.3 57.9 1.0
ND1 D:HIS487 2.3 55.0 1.0
SG D:CYS477 2.4 58.7 1.0
SG D:CYS452 2.5 65.2 1.0
CB D:CYS477 3.2 55.9 1.0
CB D:CYS484 3.2 56.8 1.0
CG D:HIS487 3.3 53.3 1.0
CB D:CYS452 3.3 70.7 1.0
CE1 D:HIS487 3.4 55.0 1.0
CB D:HIS487 3.4 52.2 1.0
CA D:CYS452 3.9 72.6 1.0
N D:CYS484 4.0 56.7 1.0
CA D:CYS484 4.2 56.5 1.0
N D:HIS487 4.4 54.2 1.0
CA D:CYS477 4.4 55.6 1.0
CD2 D:HIS487 4.4 54.6 1.0
N D:CYS477 4.5 55.8 1.0
NE2 D:HIS487 4.5 55.5 1.0
CA D:HIS487 4.5 53.2 1.0
N D:CYS452 4.7 71.0 1.0
CB D:THR475 4.8 53.1 1.0
OG1 D:THR475 4.8 53.9 1.0
C D:CYS484 4.9 56.9 1.0
O D:CYS484 4.9 57.1 1.0

Zinc binding site 3 out of 3 in 5smf

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Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z56791867


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 Z56791867 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:68.2
occ:1.00
 ND1 D:HIS229 1.9 68.2 1.0
SG D:CYS207 2.3 78.3 1.0
SG D:CYS226 2.4 69.2 1.0
SG D:CYS210 2.4 74.7 1.0
CE1 D:HIS229 2.8 68.6 1.0
CB D:CYS207 3.1 77.7 1.0
CG D:HIS229 3.1 66.0 1.0
CB D:CYS210 3.4 72.8 1.0
CB D:CYS226 3.5 61.9 1.0
CB D:HIS229 3.6 63.8 1.0
N D:CYS210 3.8 73.8 1.0
NE2 D:HIS229 3.9 68.2 1.0
N D:CYS226 4.0 60.6 1.0
CA D:CYS210 4.1 73.0 1.0
CD2 D:HIS229 4.1 67.0 1.0
CA D:CYS226 4.4 59.7 1.0
C D:LEU209 4.4 75.0 1.0
N D:HIS229 4.4 61.5 1.0
NH1 D:ARG212 4.5 75.8 1.0
CA D:CYS207 4.5 78.2 1.0
CB D:LEU209 4.6 75.9 1.0
C D:CYS210 4.6 72.4 1.0
CA D:HIS229 4.7 62.4 1.0
CB D:ARG212 4.7 68.8 1.0
N D:LEU209 4.8 76.8 1.0
CD D:ARG212 4.8 73.3 1.0
CA D:LEU209 4.8 75.8 1.0
CB D:HIS228 4.9 60.4 1.0
O D:CYS210 5.0 72.7 1.0
O D:LEU209 5.0 75.3 1.0
C D:CYS226 5.0 57.8 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 08:02:58 2024

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