Atomistry » Zinc » PDB 5slg-5smk » 5slm
Atomistry »
  Zinc »
    PDB 5slg-5smk »
      5slm »

Zinc in PDB 5slm: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384, PDB code: 5slm 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) 69.35 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.828, 67.311, 138.691, 90, 90, 90
R / Rfree (%) 25.8 / 30.7

Other elements in 5slm:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384 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 Z28290384 (pdb code 5slm). 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 Z28290384, PDB code: 5slm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slm

Go back to Zinc Binding Sites List in 5slm
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384


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 Z28290384 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:42.1
occ:1.00
ND1 D:HIS264 2.0 54.2 1.0
NE2 D:HIS257 2.2 50.6 1.0
SG D:CYS279 2.3 40.8 1.0
SG D:CYS261 2.4 49.0 1.0
CE1 D:HIS264 2.9 54.6 1.0
CD2 D:HIS257 3.0 49.3 1.0
CB D:CYS261 3.1 50.0 1.0
CB D:CYS279 3.1 40.0 1.0
CG D:HIS264 3.2 53.5 1.0
CE1 D:HIS257 3.3 50.7 1.0
CB D:HIS264 3.6 54.3 1.0
NE2 D:HIS264 4.1 54.4 1.0
CG D:HIS257 4.2 48.6 1.0
CD2 D:HIS264 4.2 53.7 1.0
ND1 D:HIS257 4.3 50.3 1.0
N D:HIS264 4.4 55.1 1.0
N D:ASP415 4.5 39.8 1.0
CA D:CYS261 4.5 51.0 1.0
CA D:CYS279 4.6 39.9 1.0
CA D:HIS264 4.7 55.8 1.0
O D:HOH727 4.7 48.4 1.0
SG D:CYS414 4.8 42.0 0.6
CA D:CYS414 4.8 39.6 0.4
CA D:CYS414 4.8 39.6 0.6
O D:GLY413 5.0 39.3 1.0

Zinc binding site 2 out of 3 in 5slm

Go back to Zinc Binding Sites List in 5slm
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384


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 Z28290384 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:52.8
occ:1.00
ND1 D:HIS487 2.2 52.0 1.0
SG D:CYS484 2.3 47.3 1.0
SG D:CYS477 2.4 46.5 1.0
SG D:CYS452 2.5 59.5 1.0
CE1 D:HIS487 3.2 52.2 1.0
CB D:CYS477 3.2 43.7 1.0
CG D:HIS487 3.2 49.5 1.0
CB D:CYS484 3.3 47.3 1.0
CB D:CYS452 3.4 63.4 1.0
CB D:HIS487 3.6 47.0 1.0
CA D:CYS452 3.9 65.1 1.0
N D:CYS484 4.1 47.2 1.0
CA D:CYS484 4.3 47.3 1.0
NE2 D:HIS487 4.3 51.9 1.0
CD2 D:HIS487 4.3 50.6 1.0
N D:CYS477 4.3 44.2 1.0
CA D:CYS477 4.4 43.5 1.0
N D:HIS487 4.5 46.4 1.0
CA D:HIS487 4.7 46.1 1.0
CB D:THR475 4.7 45.0 1.0
OG1 D:THR475 4.7 45.2 1.0
N D:CYS452 4.8 63.8 1.0
O D:HOH886 4.9 43.8 1.0
O D:CYS484 4.9 48.4 1.0
C D:CYS484 5.0 48.3 1.0

Zinc binding site 3 out of 3 in 5slm

Go back to Zinc Binding Sites List in 5slm
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z28290384


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 Z28290384 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:52.9
occ:1.00
ND1 D:HIS229 2.0 50.2 1.0
SG D:CYS207 2.3 57.9 1.0
SG D:CYS210 2.5 58.5 1.0
SG D:CYS226 2.5 53.4 1.0
CE1 D:HIS229 2.9 50.9 1.0
CG D:HIS229 3.1 49.0 1.0
CB D:CYS207 3.1 56.5 1.0
CB D:CYS226 3.5 48.8 1.0
CB D:HIS229 3.5 47.8 1.0
CB D:CYS210 3.6 57.8 1.0
N D:CYS210 3.8 57.6 1.0
N D:CYS226 3.9 47.9 1.0
NE2 D:HIS229 4.1 51.1 1.0
CD2 D:HIS229 4.2 50.1 1.0
CA D:CYS210 4.2 57.5 1.0
N D:HIS229 4.3 47.0 1.0
CA D:CYS226 4.3 47.6 1.0
NH1 D:ARG212 4.4 61.2 1.0
C D:LEU209 4.5 58.4 1.0
CA D:HIS229 4.5 47.1 1.0
CA D:CYS207 4.5 56.7 1.0
CB D:LEU209 4.6 58.5 1.0
CB D:ARG212 4.7 54.5 1.0
N D:LEU209 4.8 58.3 1.0
C D:CYS210 4.8 57.8 1.0
CA D:LEU209 4.8 58.4 1.0
CB D:HIS228 4.8 46.8 1.0
C D:CYS226 4.9 46.6 1.0
CD D:ARG212 4.9 58.4 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 07:51:02 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy