Zinc in PDB 8g62: Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004

Enzymatic activity of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004

All present enzymatic activity of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004:
3.4.19.12; 3.4.22.69;

Protein crystallography data

The structure of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004, PDB code: 8g62 was solved by J.Osipiuk, C.Tesar, M.Endres, R.Jedrzejczak, D.Luci, S.Kales, A.Simeonov, G.Rai, N.Drayman, S.Tay, S.Oakes, M.Rosner, B.Chen, N.Dulin, J.Solway, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid), Center For Structural Biology Of Infectious Diseases (Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.06 / 2.17
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 170.02, 170.02, 97.588, 90, 90, 90
R / Rfree (%) 18 / 21.4

Other elements in 8g62:

The structure of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 (pdb code 8g62). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004, PDB code: 8g62:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8g62

Go back to Zinc Binding Sites List in 8g62
Zinc binding site 1 out of 3 in the Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:71.7
occ:1.00
SG A:CYS224 2.2 65.1 1.0
SG A:CYS189 2.3 66.9 1.0
SG A:CYS192 2.3 78.3 1.0
SG A:CYS226 2.3 75.3 1.0
CB A:CYS224 3.2 63.4 1.0
CB A:CYS226 3.3 76.7 1.0
CB A:CYS192 3.3 76.4 1.0
CB A:CYS189 3.4 67.2 1.0
N A:CYS226 3.9 71.3 1.0
N A:CYS192 4.0 82.5 1.0
CA A:CYS226 4.2 75.3 1.0
CA A:CYS192 4.3 79.7 1.0
CB A:THR191 4.4 86.2 1.0
CA A:CYS224 4.4 64.8 1.0
C A:CYS224 4.6 65.0 1.0
O A:HOH633 4.6 61.3 1.0
N A:THR225 4.7 63.6 1.0
CA A:CYS189 4.8 69.0 1.0
CG2 A:THR191 4.9 86.6 1.0
C A:THR191 5.0 84.1 1.0

Zinc binding site 2 out of 3 in 8g62

Go back to Zinc Binding Sites List in 8g62
Zinc binding site 2 out of 3 in the Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:69.6
occ:1.00
SG B:CYS226 2.3 71.6 1.0
SG B:CYS224 2.3 61.2 1.0
SG B:CYS189 2.3 64.8 1.0
SG B:CYS192 2.4 75.1 1.0
CB B:CYS226 3.0 69.3 1.0
CB B:CYS224 3.2 58.1 1.0
CB B:CYS192 3.3 71.8 1.0
CB B:CYS189 3.4 65.2 1.0
N B:CYS226 3.9 64.8 1.0
CA B:CYS226 4.1 67.3 1.0
N B:CYS192 4.1 77.2 1.0
O B:HOH612 4.3 55.4 1.0
CA B:CYS192 4.3 74.1 1.0
CB B:THR191 4.5 80.1 1.0
CA B:CYS224 4.5 56.5 1.0
C B:CYS224 4.6 60.5 1.0
N B:THR225 4.7 61.8 1.0
CA B:CYS189 4.8 65.1 1.0
C B:CYS226 4.9 69.0 1.0
CE B:LYS228 4.9 69.2 0.4

Zinc binding site 3 out of 3 in 8g62

Go back to Zinc Binding Sites List in 8g62
Zinc binding site 3 out of 3 in the Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:70.5
occ:1.00
SG C:CYS224 2.3 59.6 1.0
SG C:CYS189 2.3 68.8 1.0
SG C:CYS192 2.4 77.2 1.0
SG C:CYS226 2.4 69.7 1.0
CB C:CYS224 3.2 58.5 1.0
CB C:CYS226 3.2 69.2 1.0
CB C:CYS192 3.2 76.3 1.0
CB C:CYS189 3.4 67.7 1.0
N C:CYS226 3.9 65.4 1.0
N C:CYS192 4.0 79.3 1.0
CA C:CYS226 4.1 69.9 1.0
CA C:CYS192 4.3 78.7 1.0
CA C:CYS224 4.5 58.5 1.0
CB C:THR191 4.6 81.9 1.0
C C:CYS224 4.6 60.1 1.0
N C:THR225 4.7 61.0 1.0
CA C:CYS189 4.8 69.3 1.0

Reference:

J.Osipiuk, C.Tesar, M.Endres, R.Jedrzejczak, D.Luci, S.Kales, A.Simeonov, G.Rai, N.Drayman, S.Tay, S.Oakes, M.Rosner, B.Chen, N.Dulin, J.Solway, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid), Center For Structural Biology Of Infectiousdiseases (Csbid). Papain-Like Protease of Sars Cov-2 in Complex with Remodilin Ncgc 390004 To Be Published.
Page generated: Sat Apr 8 09:08:20 2023

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