Zinc in PDB 7jiw: The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER530

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER530, PDB code: 7jiw 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)	45.51 / 2.30
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	113.648, 113.648, 220.574, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER530 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_SNYDER530 (pdb code 7jiw). 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_SNYDER530, PDB code: 7jiw:
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_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 in Complex with PLP_SNYDER530 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:0.6 occ:1.00 SG A:CYS192 2.4 0.6 1.0 SG A:CYS224 2.4 0.4 1.0 SG A:CYS226 2.5 0.9 1.0 SG A:CYS189 2.8 0.6 1.0 CB A:CYS192 2.9 0.5 1.0 CB A:CYS226 3.0 0.8 1.0 CB A:CYS189 3.5 0.4 1.0 N A:CYS192 3.6 0.9 1.0 CB A:CYS224 3.7 0.1 1.0 OG1 A:THR191 3.7 0.8 0.4 CA A:CYS192 3.8 0.7 1.0 CA A:CYS226 4.2 0.9 1.0 N A:CYS226 4.3 0.5 1.0 C A:THR191 4.8 1.0 1.0 CB A:THR191 4.8 0.4 0.4 CB A:THR191 4.8 0.5 0.6 CA A:CYS224 5.0 0.6 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_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 in Complex with PLP_SNYDER530 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:82.4 occ:1.00 ND1 A:HIS89 2.1 69.2 1.0 OD2 A:ASP108 2.1 73.2 1.0 CL A:CL509 2.6 0.5 1.0 CE1 A:HIS89 3.0 72.8 1.0 CG A:ASP108 3.1 70.4 1.0 CG A:HIS89 3.1 67.3 1.0 OD1 A:ASP108 3.3 76.3 1.0 CB A:HIS89 3.4 66.1 1.0 NE2 A:HIS89 4.2 66.2 1.0 CD2 A:HIS89 4.2 64.4 1.0 CA A:HIS89 4.2 69.1 1.0 CG1 A:VAL159 4.3 67.5 1.0 CB A:ASP108 4.4 67.7 1.0 NE1 A:TRP93 4.5 73.8 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_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 in Complex with PLP_SNYDER530 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:76.9 occ:1.00 ND1 A:HIS73 2.1 61.2 1.0 CL A:CL506 2.2 76.1 1.0 CL A:CL507 2.4 81.8 1.0 CG A:HIS73 3.1 62.8 1.0 CE1 A:HIS73 3.1 65.4 1.0 CB A:HIS73 3.3 63.8 1.0 CB A:ASN128 4.1 74.4 1.0 CD2 A:HIS73 4.2 63.9 1.0 NE2 A:HIS73 4.2 65.3 1.0 CA A:HIS73 4.6 64.0 1.0 CG A:PRO129 4.7 63.9 1.0 O A:HIS73 4.7 70.3 1.0 ND2 A:ASN128 4.8 74.1 1.0 CD A:PRO129 4.8 66.0 1.0 CG A:ASN128 4.9 77.1 1.0 N A:PRO129 5.0 66.1 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_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 in Complex with PLP_SNYDER530 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:75.8 occ:1.00 ND1 A:HIS272 2.0 92.2 1.0 O A:HOH621 2.1 69.4 1.0 SG A:CYS111 2.4 68.1 1.0 CE1 A:HIS272 2.6 93.2 1.0 CL A:CL508 2.7 91.5 1.0 CB A:CYS111 3.1 63.9 1.0 CG A:HIS272 3.3 95.2 1.0 NE2 A:HIS272 3.9 94.3 1.0 N A:CYS111 3.9 63.8 1.0 CB A:HIS272 4.0 82.1 1.0 O A:GLY271 4.1 67.2 1.0 CA A:CYS111 4.1 64.3 1.0 O A:HOH628 4.1 78.2 1.0 CA A:HIS272 4.2 78.3 1.0 CD2 A:HIS272 4.2 94.9 1.0 OD1 A:ASN109 4.3 70.2 1.0 CA A:ASN109 4.3 66.3 1.0 CH2 A:TRP106 4.3 0.2 1.0 C A:ASN109 4.4 67.4 1.0 O A:HOH603 4.4 73.8 1.0 CZ3 A:TRP106 4.5 1.0 1.0 O A:ASN109 4.5 67.9 1.0 CZ2 A:TRP106 4.5 0.0 1.0 CE3 A:TRP106 4.8 0.2 1.0 CE2 A:TRP106 4.9 0.4 1.0 N A:TYR273 4.9 70.7 1.0 CB A:ASN109 4.9 67.5 1.0 N A:ASN110 4.9 65.7 1.0 C A:GLY271 4.9 72.1 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_SNYDER530 To Be Published.