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Zinc in PDB 5slw: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1310876699

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1310876699, PDB code: 5slw 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) 69.21 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.776, 68.384, 138.415, 90, 90, 90
R / Rfree (%) 23.8 / 27.3

Other elements in 5slw:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1310876699 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

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 Z1310876699 (pdb code 5slw). 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 Z1310876699, PDB code: 5slw:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slw

Go back to Zinc Binding Sites List in 5slw
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1310876699


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 Z1310876699 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:37.5
occ:1.00
 ND1 D:HIS264 1.9 42.4 1.0
NE2 D:HIS257 2.0 42.9 1.0
SG D:CYS279 2.3 34.6 1.0
SG D:CYS261 2.4 42.4 1.0
CE1 D:HIS264 2.8 43.1 1.0
CD2 D:HIS257 2.9 42.2 1.0
CG D:HIS264 3.1 42.1 1.0
CE1 D:HIS257 3.1 42.8 1.0
CB D:CYS261 3.1 41.5 1.0
CB D:CYS279 3.1 32.5 1.0
CB D:HIS264 3.6 44.5 1.0
NE2 D:HIS264 4.0 43.4 1.0
CG D:HIS257 4.1 41.2 1.0
CD2 D:HIS264 4.1 42.7 1.0
ND1 D:HIS257 4.2 42.5 1.0
N D:HIS264 4.3 45.7 1.0
N D:ASP415 4.5 36.0 1.0
CA D:CYS261 4.6 42.3 1.0
CA D:HIS264 4.6 46.6 1.0
CA D:CYS279 4.6 32.5 1.0
SG D:CYS414 4.9 40.5 0.6
CA D:CYS414 4.9 36.3 0.6
CA D:CYS414 4.9 36.1 0.4
O D:HOH729 5.0 39.5 1.0
C D:CYS261 5.0 42.4 1.0

Zinc binding site 2 out of 3 in 5slw

Go back to Zinc Binding Sites List in 5slw
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1310876699


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 Z1310876699 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:43.0
occ:1.00
 ND1 D:HIS487 2.2 40.3 1.0
SG D:CYS484 2.2 39.9 1.0
SG D:CYS452 2.4 50.3 1.0
SG D:CYS477 2.4 40.3 1.0
CE1 D:HIS487 3.1 40.4 1.0
CB D:CYS477 3.1 36.5 1.0
CB D:CYS452 3.2 52.7 1.0
CG D:HIS487 3.2 38.8 1.0
CB D:CYS484 3.3 39.9 1.0
CB D:HIS487 3.5 38.0 1.0
CA D:CYS452 3.8 54.0 1.0
N D:CYS484 4.0 40.3 1.0
CA D:CYS484 4.2 40.5 1.0
NE2 D:HIS487 4.3 40.5 1.0
CD2 D:HIS487 4.3 39.6 1.0
CA D:CYS477 4.3 36.3 1.0
N D:CYS477 4.3 37.0 1.0
N D:HIS487 4.4 38.9 1.0
N D:CYS452 4.6 52.7 1.0
CA D:HIS487 4.6 38.6 1.0
CB D:THR475 4.8 37.5 1.0
OG1 D:THR475 4.8 38.3 1.0
C D:CYS484 4.9 41.7 1.0
O D:CYS484 4.9 42.3 1.0
O D:HOH790 5.0 39.8 1.0

Zinc binding site 3 out of 3 in 5slw

Go back to Zinc Binding Sites List in 5slw
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1310876699


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 Z1310876699 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:48.6
occ:1.00
 ND1 D:HIS229 2.1 45.7 1.0
SG D:CYS210 2.3 55.8 1.0
SG D:CYS207 2.3 51.2 1.0
SG D:CYS226 2.4 47.4 1.0
CE1 D:HIS229 3.0 46.2 1.0
CB D:CYS207 3.1 50.7 1.0
CG D:HIS229 3.2 43.7 1.0
CB D:CYS210 3.4 53.0 1.0
CB D:CYS226 3.5 41.7 1.0
CB D:HIS229 3.6 41.2 1.0
N D:CYS210 3.9 52.1 1.0
N D:CYS226 4.0 40.9 1.0
CA D:CYS210 4.1 52.1 1.0
NE2 D:HIS229 4.2 46.4 1.0
NH1 D:ARG212 4.2 51.1 1.0
CD2 D:HIS229 4.3 45.2 1.0
C D:LEU209 4.3 52.9 1.0
CA D:CYS226 4.3 40.5 1.0
N D:HIS229 4.4 40.4 1.0
CA D:CYS207 4.6 51.0 1.0
CD D:ARG212 4.6 47.1 1.0
C D:CYS210 4.7 52.1 1.0
CA D:HIS229 4.7 40.8 1.0
CB D:LEU209 4.7 54.0 1.0
CB D:ARG212 4.8 46.6 1.0
O D:LEU209 4.8 53.2 1.0
CB D:HIS228 4.9 40.3 1.0
CA D:LEU209 4.9 53.3 1.0
N D:LEU209 4.9 53.1 1.0
O D:CYS210 4.9 52.5 1.0
C D:CYS226 5.0 39.5 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 07:56:57 2024

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