Zinc in PDB 7lfv: Crystal Structure of the Sars Cov-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251

Enzymatic activity of Crystal Structure of the Sars Cov-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251

All present enzymatic activity of Crystal Structure of the Sars Cov-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251:
3.4.19.12; 3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Sars Cov-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251, PDB code: 7lfv was solved by S.K.Olsen, Z.Lv, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.34 / 2.23
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.61, 103.61, 265.354, 90, 90, 120
R / Rfree (%) 19.7 / 23.5

Other elements in 7lfv:

The structure of Crystal Structure of the Sars Cov-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Sars Cov-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251 (pdb code 7lfv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Sars Cov-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251, PDB code: 7lfv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7lfv

Go back to Zinc Binding Sites List in 7lfv
Zinc binding site 1 out of 2 in the Crystal Structure of the Sars Cov-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251


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-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:122.8
occ:1.00
SG B:CYS227 2.5 164.2 1.0
CB B:CYS227 2.6 160.9 1.0
SG B:CYS225 2.7 135.4 1.0
SG B:CYS190 3.1 137.2 1.0
CB B:CYS190 3.2 133.8 1.0
CB B:CYS193 3.4 145.6 1.0
SG B:CYS193 3.4 160.1 1.0
CB B:CYS225 3.7 137.4 1.0
N B:CYS227 3.7 153.0 1.0
CA B:CYS227 3.7 157.4 1.0
N B:CYS193 4.0 148.7 1.0
CA B:CYS193 4.3 150.0 1.0
CB B:HIS192 4.7 144.6 1.0
CA B:CYS190 4.8 130.3 1.0
C B:CYS227 4.8 156.8 1.0
N B:GLY228 4.8 150.9 1.0
ND1 B:HIS192 4.8 146.7 1.0
N B:VAL226 4.9 138.0 1.0
CA B:CYS225 4.9 133.2 1.0
C B:VAL226 5.0 151.4 1.0
C B:HIS192 5.0 150.0 1.0

Zinc binding site 2 out of 2 in 7lfv

Go back to Zinc Binding Sites List in 7lfv
Zinc binding site 2 out of 2 in the Crystal Structure of the Sars Cov-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251


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-1 Papain-Like Protease in Complex with Peptide Inhibitor VIR251 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:92.4
occ:1.00
SG A:CYS225 2.3 87.9 1.0
SG A:CYS227 2.3 109.0 1.0
SG A:CYS190 2.5 81.7 1.0
SG A:CYS193 2.5 91.8 1.0
CB A:CYS227 2.9 106.3 1.0
CB A:CYS190 3.4 74.1 1.0
CB A:CYS193 3.6 85.2 1.0
CB A:CYS225 3.7 87.8 1.0
N A:CYS227 3.9 101.1 1.0
CA A:CYS227 4.0 103.7 1.0
N A:CYS193 4.4 84.0 1.0
CA A:CYS193 4.7 84.5 1.0
CB A:HIS192 4.8 88.7 1.0
C A:CYS225 4.8 94.6 1.0
CA A:CYS225 4.9 86.9 1.0
CA A:CYS190 4.9 72.6 1.0
N A:VAL226 4.9 99.5 1.0
C A:CYS227 4.9 104.0 1.0

Reference:

S.Patchett, Z.Lv, W.Rut, M.Bekes, M.Drag, S.K.Olsen, T.T.Huang. A Molecular Sensor Determines the Ubiquitin Substrate Specificity of Sars-Cov-2 Papain-Like Protease. Cell Rep V. 36 09754 2021.
ISSN: ESSN 2211-1247
PubMed: 34547223
DOI: 10.1016/J.CELREP.2021.109754
Page generated: Thu Nov 25 10:56:38 2021

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