Zinc in PDB 6wuu: Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250

Enzymatic activity of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250

All present enzymatic activity of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250:
3.4.19.12;

Protein crystallography data

The structure of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250, PDB code: 6wuu was solved by Z.Lv, S.K.Olsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.85 / 2.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.425, 189.693, 63.118, 90.00, 98.66, 90.00
R / Rfree (%) 19.5 / 23

Other elements in 6wuu:

The structure of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 (pdb code 6wuu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250, PDB code: 6wuu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6wuu

Go back to Zinc Binding Sites List in 6wuu
Zinc binding site 1 out of 4 in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:1.0
occ:1.00
SG A:CYS189 2.3 0.1 1.0
SG A:CYS226 2.3 0.8 1.0
SG A:CYS192 2.3 0.3 1.0
SG A:CYS224 2.4 0.5 1.0
CB A:CYS192 3.0 0.5 1.0
CB A:CYS189 3.1 96.6 1.0
CB A:CYS224 3.3 0.9 1.0
CB A:CYS226 3.3 0.2 1.0
N A:CYS192 4.1 0.1 1.0
CA A:CYS192 4.2 0.5 1.0
N A:CYS226 4.2 0.8 1.0
CA A:CYS226 4.4 0.3 1.0
CA A:CYS189 4.6 92.1 1.0
CA A:CYS224 4.7 0.1 1.0
OG1 A:THR191 4.9 0.1 1.0
CE A:LYS228 4.9 0.1 1.0
CG A:LYS228 4.9 0.3 1.0
N A:THR225 5.0 0.1 1.0

Zinc binding site 2 out of 4 in 6wuu

Go back to Zinc Binding Sites List in 6wuu
Zinc binding site 2 out of 4 in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:0.7
occ:1.00
SG B:CYS192 2.1 0.0 1.0
SG B:CYS189 2.4 83.8 1.0
SG B:CYS226 2.4 0.0 1.0
SG B:CYS224 2.4 0.1 1.0
CB B:CYS192 3.1 0.2 1.0
CB B:CYS189 3.2 86.0 1.0
CB B:CYS224 3.4 0.9 1.0
CB B:CYS226 3.6 0.6 1.0
N B:CYS192 3.8 0.5 1.0
CA B:CYS192 4.0 0.6 1.0
OG1 B:THR191 4.1 99.1 1.0
N B:CYS226 4.3 0.5 1.0
CA B:CYS226 4.5 0.4 1.0
CA B:CYS189 4.7 88.7 1.0
CA B:CYS224 4.8 0.5 1.0
CG B:LYS228 4.9 0.5 1.0
C B:THR191 4.9 0.6 1.0

Zinc binding site 3 out of 4 in 6wuu

Go back to Zinc Binding Sites List in 6wuu
Zinc binding site 3 out of 4 in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:0.3
occ:1.00
SG C:CYS192 2.2 0.7 1.0
SG C:CYS189 2.2 1.0 1.0
SG C:CYS226 2.3 0.7 1.0
SG C:CYS224 2.4 0.8 1.0
CB C:CYS192 3.1 0.8 1.0
CB C:CYS189 3.1 0.5 1.0
CB C:CYS226 3.3 0.7 1.0
CB C:CYS224 3.4 0.8 1.0
N C:CYS192 4.0 0.9 1.0
CA C:CYS192 4.1 0.2 1.0
N C:CYS226 4.2 0.1 1.0
CA C:CYS226 4.3 0.6 1.0
CA C:CYS189 4.6 0.2 1.0
OG1 C:THR191 4.6 0.7 1.0
CA C:CYS224 4.8 0.3 1.0
CG C:LYS228 4.8 0.3 1.0
O C:LYS228 5.0 0.1 1.0

Zinc binding site 4 out of 4 in 6wuu

Go back to Zinc Binding Sites List in 6wuu
Zinc binding site 4 out of 4 in the Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Sars Cov-2 Papain-Like Protease in Complex with Peptide Inhibitor VIR250 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:0.7
occ:1.00
SG D:CYS192 2.3 0.8 1.0
SG D:CYS226 2.3 0.3 1.0
SG D:CYS189 2.4 0.1 1.0
SG D:CYS224 2.4 0.8 1.0
CB D:CYS189 3.2 0.3 1.0
CB D:CYS192 3.2 0.7 1.0
CB D:CYS224 3.3 0.6 1.0
CB D:CYS226 3.5 0.7 1.0
N D:CYS192 4.3 0.7 1.0
CA D:CYS192 4.4 0.2 1.0
N D:CYS226 4.5 0.2 1.0
CA D:CYS226 4.6 0.8 1.0
CA D:CYS189 4.6 0.3 1.0
CG D:LYS228 4.7 0.4 1.0
O D:LYS228 4.7 0.2 1.0
CA D:CYS224 4.8 0.6 1.0
OG1 D:THR191 4.9 0.5 1.0
N D:GLY227 4.9 0.5 1.0
CE D:LYS228 4.9 0.1 1.0

Reference:

W.Rut, Z.Lv, M.Zmudzinski, S.Patchett, D.Nayak, S.J.Snipas, F.El Oualid, T.T.Huang, M.Bekes, M.Drag, S.K.Olsen. Activity Profiling and Structures of Inhibitor-Bound Sars-Cov-2-Plpro Protease Provides A Framework For Anti-Covid-19 Drug Design To Be Published.
Page generated: Wed Dec 16 13:06:48 2020

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