Zinc in PDB 7jiv: The Crystal Structure of Papain-Like Protease of Sars Cov-2 , C111S Mutant, in Complex with PLP_SNYDER530

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 , C111S Mutant, in Complex with PLP_SNYDER530, PDB code: 7jiv 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)	45.42 / 2.05
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	113.582, 113.582, 220.027, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 20.1

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 , C111S Mutant, in Complex with PLP_SNYDER530 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_SNYDER530 (pdb code 7jiv). 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_SNYDER530, PDB code: 7jiv:
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_SNYDER530


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_SNYDER530 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.2 occ:1.00 SG A:CYS224 2.3 94.3 1.0 SG A:CYS192 2.5 88.9 1.0 SG A:CYS226 2.6 0.6 1.0 SG A:CYS189 2.7 0.8 1.0 CB A:CYS192 2.8 95.7 1.0 CB A:CYS226 2.8 0.9 1.0 CB A:CYS189 3.4 97.6 1.0 N A:CYS192 3.6 0.0 1.0 CB A:CYS224 3.7 97.5 1.0 CA A:CYS192 3.7 0.1 1.0 CA A:CYS226 4.0 0.5 1.0 N A:CYS226 4.1 0.8 1.0 CB A:THR191 4.7 0.8 1.0 C A:THR191 4.8 0.5 1.0 CA A:CYS189 4.9 97.4 1.0 C A:CYS226 4.9 0.2 1.0 C A:CYS192 5.0 97.4 1.0 CA A:CYS224 5.0 99.6 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_SNYDER530


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_SNYDER530 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:0.7 occ:1.00 NE2 A:HIS17 1.8 90.2 1.0 OE2 A:GLU67 2.3 66.9 1.0 CE1 A:HIS17 2.7 85.8 1.0 CD2 A:HIS17 2.9 88.2 1.0 CD A:GLU67 3.0 63.2 1.0 OE1 A:GLU67 3.0 61.9 1.0 CG2 A:THR63 3.4 62.0 1.0 ND1 A:HIS17 3.9 87.1 1.0 CG A:HIS17 4.0 88.2 1.0 CB A:ASN15 4.0 77.4 1.0 CG A:GLU67 4.4 59.1 1.0 CD2 A:LEU64 4.5 63.6 1.0 CB A:THR63 4.8 60.0 1.0 CG A:ASN15 4.8 80.7 1.0 CL A:CL507 4.9 77.9 0.7

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_SNYDER530


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_SNYDER530 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:39.8 occ:0.50 ZN A:ZN504 0.0 39.8 0.5 ZN A:ZN504 1.7 53.6 0.5 OD2 A:ASP108 2.1 51.7 1.0 ND1 A:HIS89 2.1 48.3 1.0 O A:HOH733 2.2 43.9 1.0 CG A:ASP108 3.0 48.4 1.0 CE1 A:HIS89 3.1 50.5 1.0 CG A:HIS89 3.2 48.0 1.0 OD1 A:ASP108 3.2 49.0 1.0 CB A:HIS89 3.5 47.6 1.0 O A:HOH607 3.7 63.1 1.0 O A:HOH730 4.0 68.8 1.0 CG1 A:VAL159 4.2 47.3 1.0 NE2 A:HIS89 4.2 49.6 1.0 CD2 A:HIS89 4.3 47.3 1.0 CB A:ASP108 4.3 45.6 1.0 CA A:HIS89 4.4 46.2 1.0 NE1 A:TRP93 4.4 47.9 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_SNYDER530


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_SNYDER530 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:53.6 occ:0.50 ZN A:ZN504 0.0 53.6 0.5 ZN A:ZN504 1.7 39.8 0.5 ND1 A:HIS89 2.2 48.3 1.0 O A:HOH733 2.2 43.9 1.0 O A:HOH730 2.3 68.8 1.0 CE1 A:HIS89 2.9 50.5 1.0 CG A:HIS89 3.3 48.0 1.0 OD2 A:ASP108 3.7 51.7 1.0 CB A:HIS89 3.8 47.6 1.0 NE2 A:HIS89 4.1 49.6 1.0 CA A:HIS89 4.2 46.2 1.0 CD2 A:HIS89 4.3 47.3 1.0 O A:HOH607 4.4 63.1 1.0 CG A:ASP108 4.7 48.4 1.0 OD1 A:ASP108 4.8 49.0 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_SNYDER530


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_SNYDER530 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:55.3 occ:1.00 ND1 A:HIS73 2.1 45.0 1.0 CL A:CL509 2.3 59.1 1.0 CL A:CL508 2.3 57.0 1.0 CG A:HIS73 3.0 46.2 1.0 CE1 A:HIS73 3.1 48.8 1.0 CB A:HIS73 3.3 45.5 1.0 CB A:ASN128 4.0 55.4 1.0 CD2 A:HIS73 4.2 49.0 1.0 NE2 A:HIS73 4.2 48.1 1.0 O A:HOH713 4.4 90.2 1.0 ND2 A:ASN128 4.6 61.6 1.0 CA A:HIS73 4.6 47.0 1.0 O A:HIS73 4.8 54.4 1.0 CG A:ASN128 4.8 59.0 1.0 CG A:PRO129 4.8 45.0 1.0 CD A:PRO129 4.9 46.2 1.0 N A:PRO129 5.0 46.8 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_SNYDER530 To Be Published.