Zinc in PDB 7jn2: The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER441

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER441, PDB code: 7jn2 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)	45.22 / 1.93
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	114.760, 114.760, 217.530, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 20.9

The structure of The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER441 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_SNYDER441 (pdb code 7jn2). 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 in Complex with PLP_SNYDER441, PDB code: 7jn2:
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 in Complex with PLP_SNYDER441


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_SNYDER441 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:85.3 occ:1.00 SG A:CYS224 2.2 84.4 1.0 SG A:CYS226 2.4 0.1 1.0 SG A:CYS192 2.4 81.2 1.0 SG A:CYS189 2.5 79.0 1.0 CB A:CYS226 2.9 0.2 1.0 CB A:CYS192 3.2 81.3 1.0 CB A:CYS189 3.3 77.5 1.0 CB A:CYS224 3.4 83.2 1.0 N A:CYS192 3.8 85.1 1.0 CA A:CYS192 4.1 84.4 1.0 CA A:CYS226 4.2 0.9 1.0 N A:CYS226 4.4 0.6 1.0 CB A:THR191 4.5 94.6 1.0 CA A:CYS224 4.7 85.8 1.0 CA A:CYS189 4.8 76.8 1.0 C A:THR191 4.9 87.5 1.0 C A:CYS224 5.0 90.2 1.0

Zinc binding site 2 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER441


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_SNYDER441 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:70.0 occ:0.50 CE1 A:HIS17 1.5 66.4 1.0 NE2 A:HIS17 1.8 63.5 1.0 OE2 A:GLU67 2.2 53.8 1.0 OE1 A:GLU67 2.7 51.7 1.0 CD A:GLU67 2.8 51.5 1.0 ND1 A:HIS17 2.8 67.6 1.0 CD2 A:HIS17 3.1 63.9 1.0 CG2 A:THR63 3.4 56.6 1.0 CG A:HIS17 3.6 66.7 1.0 CB A:ASN15 3.9 65.6 1.0 O A:HOH606 4.2 65.5 1.0 CG A:GLU67 4.3 46.9 1.0 CD2 A:LEU64 4.6 53.2 1.0 CL A:CL507 4.6 65.0 0.7 O A:HOH731 4.7 65.6 1.0 CG A:ASN15 4.7 65.2 1.0 CB A:THR63 4.8 54.3 1.0 O A:ASN15 4.9 62.0 1.0 O A:HOH681 4.9 78.6 1.0 C A:ASN15 5.0 64.2 1.0

Zinc binding site 3 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER441


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_SNYDER441 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:44.4 occ:0.50 O A:HOH732 1.8 70.7 1.0 OD2 A:ASP108 1.8 53.4 1.0 ND1 A:HIS89 1.9 51.3 1.0 O A:HOH771 2.1 54.3 1.0 CG A:ASP108 2.8 50.1 1.0 CE1 A:HIS89 2.8 52.8 1.0 OD1 A:ASP108 3.0 53.3 1.0 CG A:HIS89 3.1 49.7 1.0 CB A:HIS89 3.5 48.0 1.0 NE2 A:HIS89 4.0 51.7 1.0 NE1 A:TRP93 4.0 47.1 1.0 CG1 A:VAL159 4.1 51.6 1.0 CD2 A:HIS89 4.1 51.8 1.0 CB A:ASP108 4.2 47.2 1.0 CA A:HIS89 4.3 45.7 1.0 CD1 A:TRP93 4.6 46.2 1.0 O A:HIS89 4.7 44.6 1.0 C A:HIS89 4.9 43.6 1.0 CE A:LYS92 4.9 57.4 1.0

Zinc binding site 4 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER441


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_SNYDER441 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:45.3 occ:1.00 ND1 A:HIS73 2.0 40.1 1.0 CL A:CL508 2.2 50.1 1.0 CL A:CL509 2.3 51.7 1.0 CE1 A:HIS73 3.0 42.9 1.0 CG A:HIS73 3.0 41.4 1.0 CB A:HIS73 3.3 39.9 1.0 O A:HOH604 4.0 65.2 1.0 NE2 A:HIS73 4.1 42.4 1.0 CD2 A:HIS73 4.1 42.7 1.0 CB A:ASN128 4.1 47.2 1.0 CA A:HIS73 4.7 39.8 1.0 OXT A:ACT511 4.8 79.1 1.0 O A:HIS73 4.8 41.6 1.0 CG A:PRO129 4.9 42.6 1.0 CD A:PRO129 4.9 42.0 1.0 N A:PRO129 5.0 40.7 1.0

Zinc binding site 5 out of 5 in the The Crystal Structure of Papain-Like Protease of Sars Cov-2 in Complex with PLP_SNYDER441


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 in Complex with PLP_SNYDER441 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn506 b:55.8 occ:1.00 O A:HOH718 2.0 68.8 1.0 ND1 A:HIS272 2.2 70.3 1.0 CL A:CL510 2.2 64.7 1.0 SG A:CYS111 2.2 43.3 1.0 CB A:CYS111 3.0 44.3 1.0 CE1 A:HIS272 3.2 69.8 1.0 CG A:HIS272 3.2 63.0 1.0 CB A:HIS272 3.5 55.5 1.0 CA A:HIS272 3.7 50.5 1.0 O A:GLY271 4.2 50.2 1.0 N A:CYS111 4.2 43.6 1.0 CA A:CYS111 4.2 43.3 1.0 NE2 A:HIS272 4.3 63.1 1.0 CD2 A:HIS272 4.3 66.7 1.0 N A:TYR273 4.4 44.5 1.0 C A:HIS272 4.6 48.4 1.0 N A:HIS272 4.8 50.7 1.0 C A:GLY271 4.9 52.3 1.0 C A:ASN109 4.9 42.4 1.0 O A:HOH704 4.9 44.4 1.0 O A:ASN109 5.0 42.2 1.0 CA A:ASN109 5.0 45.1 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_SNYDER441 To Be Published.