Zinc in PDB 7jir: The Crystal Structure of Papain-Like Protease of Sars Cov-2 , C111S Mutant, in Complex with PLP_SNYDER457

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 , C111S Mutant, in Complex with PLP_SNYDER457, PDB code: 7jir 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)	49.65 / 2.09
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	113.864, 113.864, 219.576, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 20

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 , C111S Mutant, in Complex with PLP_SNYDER457 also contains other interesting chemical elements:

Chlorine

(Cl)

4 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_SNYDER457 (pdb code 7jir). 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_SNYDER457, PDB code: 7jir:
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_SNYDER457


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_SNYDER457 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.1 occ:1.00 SG A:CYS192 2.3 0.3 1.0 SG A:CYS224 2.6 0.8 1.0 SG A:CYS226 2.7 0.6 1.0 CB A:CYS226 2.9 0.4 1.0 CB A:CYS192 2.9 0.9 1.0 SG A:CYS189 3.1 1.0 1.0 N A:CYS192 3.2 0.3 1.0 CA A:CYS192 3.6 0.2 1.0 CB A:CYS189 3.7 0.4 1.0 CA A:CYS226 4.1 0.5 1.0 N A:CYS226 4.2 0.5 1.0 CB A:CYS224 4.2 0.7 1.0 CB A:THR191 4.3 0.7 1.0 C A:THR191 4.3 0.7 1.0 CA A:THR191 4.7 0.5 1.0 C A:CYS192 4.7 0.5 1.0 N A:THR191 4.9 0.3 1.0 N A:GLY193 4.9 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_SNYDER457


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_SNYDER457 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:100.0 occ:1.00 NE2 A:HIS17 1.8 86.1 1.0 OE2 A:GLU67 2.3 63.1 1.0 CE1 A:HIS17 2.7 78.4 1.0 OE1 A:GLU67 2.9 59.7 1.0 CD A:GLU67 2.9 61.9 1.0 CD2 A:HIS17 2.9 82.3 1.0 CG2 A:THR63 3.4 64.4 1.0 ND1 A:HIS17 3.8 80.3 1.0 CG A:HIS17 4.0 81.8 1.0 CB A:ASN15 4.0 75.4 1.0 O A:HOH604 4.2 71.5 1.0 O A:HOH706 4.4 70.5 1.0 CG A:GLU67 4.4 58.4 1.0 CD2 A:LEU64 4.8 66.5 1.0 CG A:ASN15 4.8 77.6 1.0 CB A:THR63 4.8 61.9 1.0 CL A:CL506 4.9 98.1 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_SNYDER457


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_SNYDER457 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:43.9 occ:0.60 ZN A:ZN504 0.0 43.9 0.6 ZN A:ZN504 1.8 55.1 0.4 OD2 A:ASP108 2.1 50.8 1.0 ND1 A:HIS89 2.1 50.0 1.0 CL A:CL509 2.2 68.1 1.0 CG A:ASP108 3.0 47.6 1.0 CE1 A:HIS89 3.1 49.3 1.0 CG A:HIS89 3.2 52.0 1.0 OD1 A:ASP108 3.2 49.9 1.0 CB A:HIS89 3.5 49.5 1.0 O A:HOH614 3.7 63.6 1.0 CG1 A:VAL159 4.2 48.1 1.0 NE2 A:HIS89 4.2 50.1 1.0 CD2 A:HIS89 4.3 48.0 1.0 CB A:ASP108 4.3 44.2 1.0 CA A:HIS89 4.4 49.2 1.0 NE1 A:TRP93 4.5 51.0 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_SNYDER457


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_SNYDER457 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:55.1 occ:0.40 ZN A:ZN504 0.0 55.1 0.4 ZN A:ZN504 1.8 43.9 0.6 ND1 A:HIS89 2.2 50.0 1.0 CL A:CL509 2.3 68.1 1.0 CE1 A:HIS89 2.8 49.3 1.0 CG A:HIS89 3.3 52.0 1.0 OD2 A:ASP108 3.9 50.8 1.0 CB A:HIS89 3.9 49.5 1.0 NE2 A:HIS89 4.0 50.1 1.0 CA A:HIS89 4.1 49.2 1.0 CD2 A:HIS89 4.2 48.0 1.0 O A:HOH614 4.6 63.6 1.0 CG A:ASP108 4.8 47.6 1.0 OD1 A:ASP108 4.9 49.9 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_SNYDER457


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_SNYDER457 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:54.3 occ:1.00 ND1 A:HIS73 2.1 45.3 1.0 CL A:CL507 2.3 55.0 1.0 CL A:CL508 2.3 56.1 1.0 CG A:HIS73 3.0 47.3 1.0 CE1 A:HIS73 3.1 49.3 1.0 CB A:HIS73 3.3 46.9 1.0 CB A:ASN128 4.0 56.0 1.0 CD2 A:HIS73 4.2 51.0 1.0 NE2 A:HIS73 4.2 50.1 1.0 CA A:HIS73 4.6 48.3 1.0 O A:HIS73 4.7 55.1 1.0 ND2 A:ASN128 4.8 56.5 1.0 CG A:ASN128 4.8 57.6 1.0 CG A:PRO129 4.9 49.0 1.0 CD A:PRO129 4.9 49.6 1.0 O A:HOH687 4.9 73.0 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_SNYDER457 To Be Published.