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

Zinc in PDB 5slv: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942, PDB code: 5slv 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) 29.82 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.621, 68.456, 138.65, 90, 90, 90
R / Rfree (%) 24.4 / 28

Other elements in 5slv:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942 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 Z2856434942 (pdb code 5slv). 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 Z2856434942, PDB code: 5slv:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5slv

Go back to Zinc Binding Sites List in 5slv
Zinc binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:45.3
occ:1.00
ND1 D:HIS264 1.9 49.0 1.0
NE2 D:HIS257 2.1 50.6 1.0
SG D:CYS279 2.2 41.6 1.0
SG D:CYS261 2.4 56.2 1.0
CE1 D:HIS264 2.8 49.3 1.0
CD2 D:HIS257 3.0 50.0 1.0
CG D:HIS264 3.1 48.8 1.0
CB D:CYS261 3.1 55.7 1.0
CB D:CYS279 3.1 40.9 1.0
CE1 D:HIS257 3.1 50.7 1.0
CB D:HIS264 3.5 52.0 1.0
NE2 D:HIS264 4.0 49.0 1.0
CG D:HIS257 4.1 49.6 1.0
CD2 D:HIS264 4.1 48.5 1.0
ND1 D:HIS257 4.2 51.0 1.0
N D:HIS264 4.3 55.5 1.0
N D:ASP415 4.5 43.5 1.0
CA D:CYS261 4.6 56.3 1.0
CA D:HIS264 4.6 55.2 1.0
CA D:CYS279 4.6 41.0 1.0
CA D:CYS414 4.9 42.3 0.4
CA D:CYS414 4.9 43.0 0.6
SG D:CYS414 4.9 47.9 0.6
C D:CYS261 5.0 56.5 1.0

Zinc binding site 2 out of 3 in 5slv

Go back to Zinc Binding Sites List in 5slv
Zinc binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:51.8
occ:1.00
SG D:CYS484 2.2 48.3 1.0
ND1 D:HIS487 2.2 50.6 1.0
SG D:CYS452 2.3 59.8 1.0
SG D:CYS477 2.5 55.6 1.0
CB D:CYS477 3.2 49.4 1.0
CE1 D:HIS487 3.2 50.4 1.0
CG D:HIS487 3.2 48.7 1.0
CB D:CYS452 3.3 63.4 1.0
CB D:CYS484 3.3 50.7 1.0
CB D:HIS487 3.5 47.3 1.0
CA D:CYS452 3.8 64.9 1.0
N D:CYS484 4.0 51.5 1.0
CA D:CYS484 4.2 51.2 1.0
NE2 D:HIS487 4.4 50.4 1.0
N D:CYS477 4.4 48.8 1.0
CD2 D:HIS487 4.4 49.6 1.0
CA D:CYS477 4.4 48.5 1.0
N D:HIS487 4.5 47.8 1.0
N D:CYS452 4.6 63.4 1.0
CA D:HIS487 4.6 47.5 1.0
CB D:THR475 4.8 46.9 1.0
O D:CYS484 4.9 51.9 1.0
C D:CYS484 4.9 51.6 1.0
O D:HOH844 4.9 52.5 1.0
OG1 D:THR475 4.9 47.2 1.0

Zinc binding site 3 out of 3 in 5slv

Go back to Zinc Binding Sites List in 5slv
Zinc binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn603

b:58.9
occ:1.00
ND1 D:HIS229 2.0 56.6 1.0
SG D:CYS210 2.3 66.8 1.0
SG D:CYS207 2.4 60.4 1.0
SG D:CYS226 2.4 57.7 1.0
CE1 D:HIS229 2.8 57.0 1.0
CB D:CYS207 3.1 62.0 1.0
CG D:HIS229 3.2 54.6 1.0
CB D:CYS210 3.4 63.9 1.0
CB D:CYS226 3.5 51.2 1.0
CB D:HIS229 3.7 52.2 1.0
N D:CYS210 3.8 63.0 1.0
N D:CYS226 4.0 49.7 1.0
NE2 D:HIS229 4.0 57.3 1.0
CA D:CYS210 4.1 63.2 1.0
CD2 D:HIS229 4.2 56.0 1.0
CA D:CYS226 4.3 49.3 1.0
NH1 D:ARG212 4.3 63.9 1.0
C D:LEU209 4.4 63.6 1.0
N D:HIS229 4.5 50.9 1.0
CA D:CYS207 4.6 62.9 1.0
CB D:LEU209 4.7 63.9 1.0
C D:CYS210 4.7 63.5 1.0
CD D:ARG212 4.8 59.8 1.0
CB D:ARG212 4.8 58.1 1.0
CA D:HIS229 4.8 51.3 1.0
N D:LEU209 4.8 63.9 1.0
CA D:LEU209 4.8 63.7 1.0
CB D:HIS228 5.0 50.0 1.0
C D:CYS226 5.0 48.3 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 07:54:02 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