Zinc in PDB 7kok: The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496, PDB code: 7kok was solved by J.Osipiuk, C.Tesar, M.Endres, V.Lisnyak, S.Maki, C.Taylor, Y.Zhang, Z.Zhou, S.A.Azizi, K.Jones, R.Kathayat, S.A.Snyder, B.C.Dickinson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.76 / 2.00
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	113.554, 113.554, 219.682, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.1

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Zinc atom in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496 (pdb code 7kok). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496, PDB code: 7kok:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.6 occ:1.00 SG A:CYS192 2.4 99.5 1.0 SG A:CYS224 2.4 0.4 1.0 SG A:CYS226 2.6 0.5 1.0 CB A:CYS226 2.7 0.8 1.0 SG A:CYS189 2.8 0.0 1.0 CB A:CYS192 2.9 0.6 1.0 N A:CYS192 3.3 0.4 1.0 CB A:CYS189 3.4 0.0 1.0 CA A:CYS192 3.7 0.2 1.0 CB A:CYS224 3.8 0.4 1.0 CA A:CYS226 4.0 0.7 1.0 N A:CYS226 4.1 0.4 1.0 CB A:THR191 4.3 0.5 1.0 C A:THR191 4.4 0.9 1.0 CA A:THR191 4.8 0.6 1.0 C A:CYS192 4.9 0.9 1.0 CG2 A:THR191 4.9 0.4 1.0 CA A:CYS189 4.9 0.1 1.0 C A:CYS226 4.9 0.8 1.0 N A:THR191 5.0 0.1 1.0

Zinc binding site 2 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:99.0 occ:1.00 NE2 A:HIS17 1.8 83.5 1.0 OE2 A:GLU67 2.3 59.6 1.0 CE1 A:HIS17 2.7 77.2 1.0 CD2 A:HIS17 2.9 79.2 1.0 OE1 A:GLU67 2.9 58.4 1.0 CD A:GLU67 2.9 58.0 1.0 CG2 A:THR63 3.3 58.4 1.0 ND1 A:HIS17 3.8 80.1 1.0 CG A:HIS17 3.9 81.5 1.0 CB A:ASN15 4.0 74.0 1.0 O A:HOH605 4.1 65.9 1.0 CG A:GLU67 4.4 55.2 1.0 O A:HOH763 4.4 73.0 1.0 CD2 A:LEU64 4.7 62.0 1.0 CB A:THR63 4.8 57.2 1.0 CL A:CL506 4.8 71.5 0.7 CG A:ASN15 4.8 75.3 1.0

Zinc binding site 3 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:40.7 occ:0.60 ZN A:ZN504 0.0 40.7 0.6 ZN A:ZN504 1.8 54.1 0.4 OD2 A:ASP108 2.0 51.1 1.0 ND1 A:HIS89 2.1 47.9 1.0 O A:HOH776 2.3 37.9 1.0 CG A:ASP108 3.0 46.3 1.0 CE1 A:HIS89 3.0 49.5 1.0 CG A:HIS89 3.1 49.4 1.0 OD1 A:ASP108 3.3 46.8 1.0 CB A:HIS89 3.5 47.2 1.0 O A:HOH617 3.8 60.4 1.0 O A:HOH749 4.0 65.3 1.0 O A:HOH796 4.0 69.5 1.0 NE2 A:HIS89 4.2 49.9 1.0 CG1 A:VAL159 4.2 45.9 1.0 CD2 A:HIS89 4.2 46.8 1.0 CA A:HIS89 4.3 46.4 1.0 CB A:ASP108 4.3 42.1 1.0 NE1 A:TRP93 4.5 46.7 1.0

Zinc binding site 4 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:54.1 occ:0.40 ZN A:ZN504 0.0 54.1 0.4 ZN A:ZN504 1.8 40.7 0.6 O A:HOH749 2.2 65.3 1.0 O A:HOH776 2.2 37.9 1.0 ND1 A:HIS89 2.3 47.9 1.0 CE1 A:HIS89 2.9 49.5 1.0 CG A:HIS89 3.3 49.4 1.0 OD2 A:ASP108 3.8 51.1 1.0 CB A:HIS89 3.9 47.2 1.0 NE2 A:HIS89 4.1 49.9 1.0 CA A:HIS89 4.1 46.4 1.0 CD2 A:HIS89 4.3 46.8 1.0 O A:HOH796 4.3 69.5 1.0 O A:HOH617 4.6 60.4 1.0 CG A:ASP108 4.8 46.3 1.0 OD1 A:ASP108 4.9 46.8 1.0

Zinc binding site 5 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:51.8 occ:1.00 ND1 A:HIS73 2.1 44.2 1.0 CL A:CL507 2.3 53.2 1.0 CL A:CL508 2.3 53.2 1.0 CG A:HIS73 3.0 44.3 1.0 CE1 A:HIS73 3.1 46.4 1.0 CB A:HIS73 3.3 44.6 1.0 CB A:ASN128 4.0 53.7 1.0 CD2 A:HIS73 4.2 45.9 1.0 NE2 A:HIS73 4.2 46.2 1.0 CA A:HIS73 4.6 45.9 1.0 UNK A:UNX515 4.7 65.6 1.0 ND2 A:ASN128 4.8 64.6 1.0 O A:HIS73 4.8 51.7 1.0 UNK A:UNX511 4.8 68.0 1.0 CG A:ASN128 4.8 57.4 1.0 CG A:PRO129 4.8 47.4 1.0 CD A:PRO129 4.9 46.3 1.0

J.Osipiuk, C.Tesar, M.Endres, V.Lisnyak, S.Maki, C.Taylor, Y.Zhang, Z.Zhou, S.A.Azizi, K.Jones, R.Kathayat, S.A.Snyder, B.C.Dickinson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with PLP_SNYDER496 To Be Published.