Zinc in PDB 7kol: The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER496

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER496, PDB code: 7kol 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)	45.57 / 2.58
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	114.178, 114.178, 220.531, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 20.6

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

Zinc binding site 1 out of 4 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2 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 in Complex with PLP_SNYDER496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.3 occ:1.00 SG A:CYS192 2.4 1.0 1.0 SG A:CYS224 2.5 0.5 1.0 SG A:CYS226 2.6 0.5 1.0 SG A:CYS189 2.7 0.7 1.0 CB A:CYS226 2.8 0.8 1.0 CB A:CYS192 2.9 0.8 1.0 N A:CYS192 3.3 0.7 1.0 CB A:CYS189 3.3 0.2 1.0 CA A:CYS192 3.6 0.4 1.0 CB A:CYS224 3.8 0.2 1.0 CA A:CYS226 4.1 0.9 1.0 N A:CYS226 4.2 0.1 1.0 C A:THR191 4.5 1.0 1.0 CB A:THR191 4.6 0.2 1.0 C A:CYS192 4.7 0.3 1.0 CA A:CYS189 4.8 0.8 1.0 N A:GLY193 4.9 0.5 1.0 CA A:THR191 4.9 0.9 1.0

Zinc binding site 2 out of 4 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2 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 in Complex with PLP_SNYDER496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:1.0 occ:1.00 OD2 A:ASP108 2.1 89.8 1.0 ND1 A:HIS89 2.2 87.2 1.0 CL A:CL508 2.9 0.8 1.0 CG A:ASP108 3.1 88.5 1.0 CG A:HIS89 3.1 86.8 1.0 CE1 A:HIS89 3.1 89.7 1.0 OD1 A:ASP108 3.3 94.2 1.0 CB A:HIS89 3.4 85.5 1.0 CA A:HIS89 4.2 87.1 1.0 CG1 A:VAL159 4.2 89.0 1.0 CD2 A:HIS89 4.3 87.3 1.0 NE2 A:HIS89 4.3 86.8 1.0 CB A:ASP108 4.4 83.9 1.0 NE1 A:TRP93 4.5 97.4 1.0

Zinc binding site 3 out of 4 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2 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 in Complex with PLP_SNYDER496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:90.6 occ:1.00 ND1 A:HIS73 2.1 75.8 1.0 CL A:CL506 2.3 93.5 1.0 CL A:CL507 2.6 0.5 1.0 CG A:HIS73 3.0 76.0 1.0 CE1 A:HIS73 3.1 76.7 1.0 CB A:HIS73 3.2 74.9 1.0 CB A:ASN128 4.1 89.7 1.0 CD2 A:HIS73 4.2 77.5 1.0 NE2 A:HIS73 4.2 78.0 1.0 CA A:HIS73 4.6 74.5 1.0 O A:HIS73 4.7 82.9 1.0 CG A:PRO129 4.8 71.1 1.0 CD A:PRO129 4.9 72.1 1.0 ND2 A:ASN128 4.9 96.2 1.0 CG A:ASN128 5.0 95.4 1.0

Zinc binding site 4 out of 4 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2 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 in Complex with PLP_SNYDER496 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:91.6 occ:1.00 ND1 A:HIS272 1.9 0.4 1.0 SG A:CYS111 2.4 83.3 1.0 O A:HOH615 2.5 85.5 1.0 CE1 A:HIS272 2.6 0.3 1.0 CL A:CL509 2.7 0.9 1.0 CB A:CYS111 3.1 84.4 1.0 CG A:HIS272 3.2 0.2 1.0 CB A:HIS272 3.8 0.3 1.0 NE2 A:HIS272 3.9 0.6 1.0 N A:CYS111 3.9 80.6 1.0 O A:GLY271 4.0 96.3 1.0 CA A:HIS272 4.1 99.1 1.0 CA A:CYS111 4.1 81.9 1.0 CD2 A:HIS272 4.1 0.3 1.0 OD1 A:ASN109 4.2 0.2 1.0 CA A:ASN109 4.3 90.5 1.0 CH2 A:TRP106 4.3 0.2 1.0 C A:ASN109 4.4 89.3 1.0 CZ2 A:TRP106 4.4 0.2 1.0 O A:ASN109 4.6 88.7 1.0 CZ3 A:TRP106 4.6 0.9 1.0 CE2 A:TRP106 4.8 1.0 1.0 C A:GLY271 4.8 96.0 1.0 CB A:ASN109 4.8 93.6 1.0 N A:ASN110 4.8 87.2 1.0 N A:HIS272 4.9 95.2 1.0 CE3 A:TRP106 5.0 0.4 1.0 CG A:ASN109 5.0 96.9 1.0 N A:TYR273 5.0 90.3 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 in Complex with PLP_SNYDER496 To Be Published.