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Zinc in PDB 5sm2: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474, PDB code: 5sm2 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) 69.26 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.646, 67.43, 138.52, 90, 90, 90
R / Rfree (%) 25 / 27

Other elements in 5sm2:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474 also contains other interesting chemical elements:

Fluorine (F) 4 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 Z3006151474 (pdb code 5sm2). 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 Z3006151474, PDB code: 5sm2:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5sm2

Go back to Zinc Binding Sites List in 5sm2
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474


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 Z3006151474 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:38.0
occ:1.00
ND1 D:HIS264 1.9 43.1 1.0
NE2 D:HIS257 2.2 44.1 1.0
SG D:CYS279 2.3 36.9 1.0
SG D:CYS261 2.4 41.9 1.0
CE1 D:HIS264 2.8 43.4 1.0
CD2 D:HIS257 3.0 42.7 1.0
CG D:HIS264 3.1 42.9 1.0
CB D:CYS261 3.1 44.0 1.0
CB D:CYS279 3.1 33.0 1.0
CE1 D:HIS257 3.3 43.9 1.0
CB D:HIS264 3.6 45.2 1.0
NE2 D:HIS264 4.0 43.5 1.0
CD2 D:HIS264 4.2 43.0 1.0
CG D:HIS257 4.2 42.2 1.0
N D:HIS264 4.3 47.6 1.0
ND1 D:HIS257 4.4 43.4 1.0
CA D:CYS261 4.6 45.0 1.0
CA D:HIS264 4.6 47.9 1.0
N D:ASP415 4.6 36.7 1.0
CA D:CYS279 4.6 33.0 1.0
O D:HOH804 4.9 35.1 1.0
CA D:CYS414 5.0 35.9 0.4
SG D:CYS414 5.0 37.8 0.6
CA D:CYS414 5.0 35.8 0.6
C D:CYS261 5.0 45.5 1.0

Zinc binding site 2 out of 3 in 5sm2

Go back to Zinc Binding Sites List in 5sm2
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474


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 Z3006151474 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:43.8
occ:1.00
ND1 D:HIS487 2.2 42.0 1.0
SG D:CYS484 2.3 41.2 1.0
SG D:CYS452 2.4 52.4 1.0
SG D:CYS477 2.4 40.9 1.0
CG D:HIS487 3.1 39.4 1.0
CB D:CYS477 3.2 39.4 1.0
CE1 D:HIS487 3.2 41.9 1.0
CB D:CYS452 3.2 56.2 1.0
CB D:CYS484 3.3 41.2 1.0
CB D:HIS487 3.4 36.6 1.0
CA D:CYS452 3.8 58.1 1.0
N D:CYS484 3.9 40.5 1.0
CA D:CYS484 4.2 40.9 1.0
CD2 D:HIS487 4.3 40.6 1.0
N D:CYS477 4.3 40.5 1.0
NE2 D:HIS487 4.4 41.6 1.0
CA D:CYS477 4.4 39.6 1.0
N D:HIS487 4.4 37.0 1.0
CA D:HIS487 4.5 36.8 1.0
OG1 D:THR475 4.6 39.5 1.0
N D:CYS452 4.7 56.8 1.0
CB D:THR475 4.7 39.1 1.0
C D:CYS484 4.8 41.4 1.0
O D:CYS484 4.8 41.1 1.0
C D:CYS452 5.0 61.4 1.0

Zinc binding site 3 out of 3 in 5sm2

Go back to Zinc Binding Sites List in 5sm2
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z3006151474


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 Z3006151474 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:48.1
occ:1.00
ND1 D:HIS229 2.1 50.6 1.0
SG D:CYS207 2.3 51.5 1.0
SG D:CYS210 2.4 53.4 1.0
SG D:CYS226 2.4 45.4 1.0
CE1 D:HIS229 2.9 50.7 1.0
CB D:CYS207 3.0 51.4 1.0
CG D:HIS229 3.2 48.3 1.0
CB D:CYS226 3.4 41.8 1.0
CB D:CYS210 3.5 52.9 1.0
CB D:HIS229 3.7 44.7 1.0
N D:CYS210 3.8 53.3 1.0
N D:CYS226 4.0 41.1 1.0
NE2 D:HIS229 4.1 51.0 1.0
CA D:CYS210 4.1 52.8 1.0
NH1 D:ARG212 4.3 47.6 1.0
CD2 D:HIS229 4.3 49.7 1.0
CA D:CYS226 4.3 40.9 1.0
C D:LEU209 4.4 54.5 1.0
N D:HIS229 4.5 42.8 1.0
CA D:CYS207 4.5 52.3 1.0
CB D:LEU209 4.7 55.5 1.0
CD D:ARG212 4.7 47.8 1.0
C D:CYS210 4.7 53.0 1.0
CB D:ARG212 4.7 47.4 1.0
CA D:HIS229 4.8 43.3 1.0
N D:LEU209 4.8 55.0 1.0
CA D:LEU209 4.8 55.0 1.0
CB D:HIS228 4.9 41.1 1.0
C D:CYS226 5.0 39.7 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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