Zinc in PDB 7skq: Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617

All present enzymatic activity of Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617:
3.4.19.12; 3.4.22.69;

The structure of Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617, PDB code: 7skq was solved by B.Freitas, I.Durie, J.Shepard, B.O'boyle, S.Enos, S.D.Pegan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.57 / 3.16
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.385, 67.167, 165.309, 90, 90, 90
R / Rfree (%)	23 / 25.9

The binding sites of Zinc atom in the Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617 (pdb code 7skq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617, PDB code: 7skq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:66.2 occ:1.00 SG A:CYS227 2.3 65.5 1.0 SG A:CYS193 2.5 91.9 1.0 SG A:CYS190 2.5 55.5 1.0 SG A:CYS225 2.5 91.3 1.0 CB A:CYS225 3.2 73.2 1.0 CB A:CYS193 3.2 69.9 1.0 CB A:CYS190 3.3 62.0 1.0 CB A:CYS227 3.4 72.4 1.0 N A:CYS227 4.2 87.7 1.0 CG A:ARG229 4.3 72.4 1.0 CA A:CYS227 4.4 78.1 1.0 N A:CYS193 4.4 84.0 1.0 CA A:CYS193 4.5 80.2 1.0 CD A:ARG229 4.6 67.9 1.0 CA A:CYS225 4.7 77.0 1.0 CA A:CYS190 4.7 61.4 1.0 N A:VAL226 5.0 65.9 1.0

Zinc binding site 2 out of 4 in the Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:44.8 occ:1.00 OD2 A:ASP109 2.1 35.0 1.0 NE2 A:HIS90 2.3 31.2 1.0 SG B:CYS271 2.3 106.4 1.0 OD1 A:ASP109 2.6 57.8 1.0 CG A:ASP109 2.7 37.7 1.0 CD2 A:HIS90 3.1 35.0 1.0 CB B:CYS271 3.1 53.2 1.0 CE1 A:HIS90 3.4 56.6 1.0 CA B:CYS271 3.6 47.7 1.0 O B:GLN270 4.0 34.0 1.0 NE1 A:TRP94 4.0 39.9 1.0 CB A:ASP109 4.2 43.3 1.0 O B:HOH507 4.2 37.1 1.0 CG A:HIS90 4.3 36.2 1.0 CB A:ALA108 4.4 61.2 1.0 ND1 A:HIS90 4.4 38.8 1.0 ND2 B:ASN110 4.5 35.7 1.0 CD1 A:TRP94 4.6 40.7 1.0 C B:CYS271 4.6 37.5 1.0 CD1 B:LEU163 4.6 38.6 1.0 N B:CYS271 4.6 30.8 1.0 N A:ASP109 4.7 45.5 1.0 C B:GLN270 4.8 38.3 1.0 C A:ALA108 4.9 52.3 1.0 CA A:ASP109 5.0 54.1 1.0

Zinc binding site 3 out of 4 in the Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:98.7 occ:1.00 SG B:CYS227 2.3 145.8 1.0 SG B:CYS190 2.4 103.5 1.0 SG B:CYS225 2.5 95.9 1.0 SG B:CYS193 2.7 117.9 1.0 CB B:CYS225 3.4 97.6 1.0 CB B:CYS193 3.6 100.5 1.0 CB B:CYS190 3.6 87.2 1.0 CB B:CYS227 4.0 113.8 1.0 NH1 B:ARG229 4.0 104.0 1.0 N B:CYS227 4.5 108.1 1.0 CA B:CYS227 4.7 102.2 1.0 CA B:CYS225 4.8 101.0 1.0 O B:HOH502 4.8 78.8 1.0 O B:GLY228 4.8 102.0 1.0 CA B:CYS193 4.8 97.5 1.0 N B:CYS193 4.8 104.0 1.0 CA B:CYS190 5.0 80.4 1.0

Zinc binding site 4 out of 4 in the Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Btscov-RF1.2004 Papain-Like Protease Bound to the Non-Covalent Inhibitor Grl-0617 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:57.9 occ:1.00 OD2 B:ASP109 2.1 39.1 1.0 NE2 B:HIS90 2.3 48.7 1.0 SG A:CYS271 2.3 56.2 1.0 OD1 B:ASP109 2.3 62.3 1.0 CG B:ASP109 2.5 41.0 1.0 CB A:CYS271 3.1 48.3 1.0 CD2 B:HIS90 3.1 58.1 1.0 CE1 B:HIS90 3.3 66.9 1.0 CA A:CYS271 3.7 48.6 1.0 O B:HOH506 3.7 33.5 1.0 O A:GLN270 3.9 36.7 1.0 CB B:ASP109 4.0 38.6 1.0 NE1 B:TRP94 4.1 52.2 1.0 CG B:HIS90 4.3 69.4 1.0 ND1 B:HIS90 4.4 70.0 1.0 ND2 A:ASN110 4.4 36.1 1.0 N A:CYS271 4.7 45.8 1.0 C A:GLN270 4.7 48.4 1.0 C A:CYS271 4.7 56.1 1.0 N B:ASP109 4.8 50.7 1.0 CD1 B:TRP94 4.9 55.1 1.0 CB B:ALA108 4.9 64.5 1.0 CA B:ASP109 4.9 39.4 1.0 CD1 A:LEU163 5.0 38.8 1.0

B.T.Freitas, D.A.Ahiadorme, R.S.Bagul, I.A.Durie, S.Ghosh, J.Hill, N.E.Kramer, J.Murray, B.M.O'boyle, E.Onobun, M.G.Pirrone, J.D.Shepard, S.Enos, Y.P.Subedi, K.Upadhyaya, R.A.Tripp, B.S.Cummings, D.Crich, S.D.Pegan. Exploring Noncovalent Protease Inhibitors For the Treatment of Severe Acute Respiratory Syndrome and Severe Acute Respiratory Syndrome-Like Coronaviruses. Acs Infect Dis. V. 8 596 2022.
ISSN: ESSN 2373-8227
PubMed: 35199517
DOI: 10.1021/ACSINFECDIS.1C00631