Zinc in PDB 7jit: The Crystal Structure of Papain-Like Protease of Sars Cov-2 , C111S Mutant, in Complex with PLP_SNYDER495

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 , C111S Mutant, in Complex with PLP_SNYDER495, PDB code: 7jit 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)	49.67 / 1.95
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	113.913, 113.913, 219.328, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 , C111S Mutant, in Complex with PLP_SNYDER495 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_SNYDER495 (pdb code 7jit). 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_SNYDER495, PDB code: 7jit:
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_SNYDER495


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_SNYDER495 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:91.4 occ:1.00 SG A:CYS224 2.3 85.9 1.0 SG A:CYS192 2.4 87.8 1.0 SG A:CYS189 2.5 81.0 1.0 SG A:CYS226 2.7 99.8 1.0 CB A:CYS192 3.1 90.3 1.0 CB A:CYS226 3.1 0.9 1.0 CB A:CYS189 3.4 80.4 1.0 CB A:CYS224 3.5 90.5 1.0 N A:CYS192 3.5 95.3 1.0 CA A:CYS192 3.9 93.1 1.0 N A:CYS226 4.3 0.5 1.0 CA A:CYS226 4.3 0.6 1.0 CB A:THR191 4.5 0.4 1.0 C A:THR191 4.6 97.6 1.0 CA A:CYS224 4.8 90.7 1.0 CA A:CYS189 4.9 81.3 1.0 CB A:LYS228 4.9 99.0 1.0 CA A:THR191 5.0 99.0 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_SNYDER495


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_SNYDER495 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:58.8 occ:1.00 NE2 A:HIS17 2.0 56.0 1.0 O A:HOH789 2.1 61.1 1.0 O A:HOH788 2.1 57.8 1.0 OE2 A:GLU67 2.2 45.7 1.0 CD A:GLU67 2.8 41.2 1.0 OE1 A:GLU67 2.9 41.3 1.0 CE1 A:HIS17 2.9 52.9 1.0 CD2 A:HIS17 3.0 54.7 1.0 O A:HOH607 3.9 55.7 1.0 CG2 A:THR63 4.0 50.3 1.0 ND1 A:HIS17 4.0 54.0 1.0 CG A:HIS17 4.1 56.7 1.0 CB A:ASN15 4.1 55.6 1.0 CG A:GLU67 4.3 40.2 1.0 CD2 A:LEU64 4.4 51.4 1.0 CG A:ASN15 4.8 59.5 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_SNYDER495


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_SNYDER495 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:31.9 occ:0.50 ZN A:ZN504 0.0 31.9 0.5 ZN A:ZN504 1.7 40.7 0.5 O A:HOH744 2.0 39.9 1.0 ND1 A:HIS89 2.1 38.1 1.0 OD2 A:ASP108 2.2 44.0 1.0 CE1 A:HIS89 3.1 39.9 1.0 CG A:ASP108 3.1 37.4 1.0 CG A:HIS89 3.1 35.9 1.0 OD1 A:ASP108 3.3 35.1 1.0 CB A:HIS89 3.5 34.3 1.0 O A:HOH611 3.6 49.6 1.0 CG1 A:VAL159 4.1 35.3 1.0 NE2 A:HIS89 4.2 36.1 1.0 CD2 A:HIS89 4.2 36.6 1.0 CA A:HIS89 4.4 32.5 1.0 CB A:ASP108 4.4 33.3 1.0 NE1 A:TRP93 4.5 34.2 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_SNYDER495


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_SNYDER495 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:40.7 occ:0.50 ZN A:ZN504 0.0 40.7 0.5 ZN A:ZN504 1.7 31.9 0.5 ND1 A:HIS89 2.1 38.1 1.0 O A:HOH744 2.3 39.9 1.0 CE1 A:HIS89 2.9 39.9 1.0 CG A:HIS89 3.2 35.9 1.0 CB A:HIS89 3.8 34.3 1.0 OD2 A:ASP108 3.8 44.0 1.0 NE2 A:HIS89 4.0 36.1 1.0 CA A:HIS89 4.1 32.5 1.0 CD2 A:HIS89 4.2 36.6 1.0 O A:HOH611 4.4 49.6 1.0 CG A:ASP108 4.7 37.4 1.0 OD1 A:ASP108 4.8 35.1 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_SNYDER495


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_SNYDER495 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:41.2 occ:1.00 ND1 A:HIS73 2.0 32.5 1.0 CL A:CL507 2.2 58.2 1.0 CL A:CL508 2.6 63.9 1.0 CG A:HIS73 3.0 33.0 1.0 CE1 A:HIS73 3.0 34.0 1.0 CB A:HIS73 3.3 34.4 1.0 CB A:ASN128 4.0 41.2 1.0 NE2 A:HIS73 4.1 34.8 1.0 CD2 A:HIS73 4.1 34.5 1.0 CA A:HIS73 4.6 34.9 1.0 O A:HIS73 4.7 36.7 1.0 ND2 A:ASN128 4.8 42.5 1.0 CG A:PRO129 4.8 33.9 1.0 CG A:ASN128 4.8 42.2 1.0 O A:HOH781 4.9 77.6 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_SNYDER495 To Be Published.