Zinc in PDB 9i4v: Crystal Structure of the Sars-Cov-2 Helicase NSP13

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Helicase NSP13:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

The structure of Crystal Structure of the Sars-Cov-2 Helicase NSP13, PDB code: 9i4v was solved by P.Kloskowski, P.Neumann, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.60 / 2.33
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.305, 70.687, 86.225, 103.7, 95.24, 112.12
R / Rfree (%)	21.3 / 25.4

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Helicase NSP13 (pdb code 9i4v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Sars-Cov-2 Helicase NSP13, PDB code: 9i4v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:65.0 occ:1.00 ND1 A:HIS75 2.1 68.2 1.0 SG A:CYS55 2.3 67.6 1.0 SG A:CYS50 2.3 61.5 1.0 SG A:CYS72 2.3 62.1 1.0 CE1 A:HIS75 2.9 69.7 1.0 CG A:HIS75 3.2 61.2 1.0 CB A:CYS55 3.3 68.3 1.0 CB A:CYS50 3.4 70.2 1.0 CB A:CYS72 3.5 73.8 1.0 CB A:HIS75 3.7 67.4 1.0 N A:CYS72 4.0 70.7 1.0 NE2 A:HIS75 4.1 61.0 1.0 CB A:ALA52 4.2 68.8 1.0 CD2 A:HIS75 4.3 60.9 1.0 CA A:CYS72 4.3 73.7 1.0 CG2 A:VAL57 4.5 74.6 1.0 N A:HIS75 4.6 70.7 1.0 CA A:CYS55 4.7 71.0 1.0 CB A:VAL57 4.8 72.1 1.0 CA A:HIS75 4.8 73.2 1.0 CA A:CYS50 4.8 70.9 1.0 C A:CYS72 4.9 74.5 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:66.1 occ:1.00 ND1 A:HIS39 2.0 69.2 1.0 NE2 A:HIS33 2.0 73.9 1.0 SG A:CYS16 2.2 79.4 1.0 SG A:CYS19 2.4 73.9 1.0 CE1 A:HIS39 3.0 69.0 1.0 CG A:HIS39 3.0 72.7 1.0 CE1 A:HIS33 3.0 78.9 1.0 CD2 A:HIS33 3.1 73.9 1.0 CB A:HIS39 3.3 66.6 1.0 CB A:CYS19 3.4 73.2 1.0 N A:CYS19 3.4 72.8 1.0 CB A:CYS16 3.4 75.0 1.0 CA A:CYS19 3.8 69.7 1.0 NE2 A:HIS39 4.0 75.5 1.0 CD2 A:HIS39 4.1 75.8 1.0 ND1 A:HIS33 4.1 79.3 1.0 CG A:HIS33 4.2 78.9 1.0 C A:ALA18 4.3 65.8 1.0 CB A:ALA18 4.4 71.2 1.0 CB A:ALA110 4.6 78.3 1.0 CA A:ALA18 4.7 74.0 1.0 CA A:CYS16 4.8 83.0 1.0 CA A:HIS39 4.8 69.6 1.0 N A:ALA18 4.9 71.6 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:110.4 occ:1.00 SG A:CYS26 1.8 132.2 1.0 SG A:CYS29 2.1 107.2 1.0 SG A:CYS5 2.2 110.5 1.0 SG A:CYS8 2.3 128.9 1.0 CB A:CYS29 2.9 100.0 1.0 CB A:CYS26 3.1 106.1 1.0 CB A:CYS8 3.3 115.7 1.0 CB A:CYS5 3.4 106.8 1.0 N A:CYS8 3.7 111.6 1.0 N A:CYS26 3.8 100.0 1.0 CA A:CYS26 4.0 100.8 1.0 CA A:CYS8 4.1 115.6 1.0 CA A:CYS29 4.2 104.7 1.0 N A:CYS29 4.3 104.9 1.0 CB A:LEU7 4.4 104.4 1.0 C A:LEU7 4.5 111.5 1.0 N A:LEU7 4.6 111.4 1.0 CA A:LEU7 4.7 106.7 1.0 CA A:CYS5 4.7 106.7 1.0 C A:CYS26 4.8 107.3 1.0 CG A:LEU7 4.9 100.2 1.0 C A:CYS8 4.9 120.6 1.0 C A:LEU25 5.0 99.5 1.0 CD1 A:LEU7 5.0 89.4 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:44.5 occ:1.00 ND1 B:HIS39 2.0 51.3 1.0 NE2 B:HIS33 2.1 57.2 1.0 SG B:CYS16 2.3 49.0 1.0 SG B:CYS19 2.3 47.3 1.0 CD2 B:HIS33 2.9 60.2 1.0 CE1 B:HIS39 3.0 59.7 1.0 CG B:HIS39 3.0 61.3 1.0 CE1 B:HIS33 3.1 54.8 1.0 CB B:HIS39 3.3 59.8 1.0 CB B:CYS19 3.4 46.4 1.0 CB B:CYS16 3.5 51.6 1.0 N B:CYS19 3.6 55.8 1.0 CA B:CYS19 3.9 49.7 1.0 NE2 B:HIS39 4.0 63.6 1.0 CD2 B:HIS39 4.1 61.9 1.0 CG B:HIS33 4.1 58.3 1.0 ND1 B:HIS33 4.2 55.9 1.0 C B:ALA18 4.4 55.7 1.0 CB B:ALA18 4.5 52.4 1.0 CB B:ALA110 4.6 54.2 1.0 CA B:HIS39 4.8 56.1 1.0 CA B:CYS16 4.8 50.1 1.0 CA B:ALA18 4.9 52.0 1.0 N B:ALA18 5.0 50.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:70.2 occ:1.00 SG B:CYS26 1.7 78.4 1.0 SG B:CYS8 2.3 79.9 1.0 SG B:CYS29 2.3 65.8 1.0 SG B:CYS5 2.7 75.0 1.0 CB B:CYS29 3.0 63.4 1.0 CB B:CYS26 3.1 63.0 1.0 CB B:CYS5 3.3 65.4 1.0 CB B:CYS8 3.4 68.8 1.0 N B:CYS26 3.8 68.2 1.0 N B:CYS8 3.8 73.9 1.0 CA B:CYS26 4.0 64.3 1.0 N B:CYS29 4.1 63.8 1.0 CA B:CYS29 4.1 61.2 1.0 CA B:CYS8 4.2 77.1 1.0 CB B:LEU7 4.3 72.4 1.0 C B:LEU7 4.6 73.8 1.0 C B:CYS26 4.7 65.1 1.0 N B:GLY99 4.8 82.6 1.0 CA B:CYS5 4.8 64.5 1.0 CA B:GLY99 4.9 84.4 1.0 CA B:LEU7 4.9 76.1 1.0 N B:LEU7 4.9 76.6 1.0 O B:CYS26 4.9 59.5 1.0 C B:LEU25 5.0 63.0 1.0 C B:CYS8 5.0 78.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Sars-Cov-2 Helicase NSP13


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Sars-Cov-2 Helicase NSP13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn703 b:76.2 occ:1.00 ND1 B:HIS75 2.0 81.5 1.0 SG B:CYS50 2.2 79.5 1.0 SG B:CYS55 2.3 75.6 1.0 SG B:CYS72 2.4 80.3 1.0 CE1 B:HIS75 2.9 76.7 1.0 CG B:HIS75 3.1 76.5 1.0 CB B:CYS55 3.2 88.0 1.0 CB B:CYS50 3.4 74.5 1.0 CB B:CYS72 3.4 72.0 1.0 CB B:HIS75 3.6 79.7 1.0 N B:CYS72 3.9 76.3 1.0 NE2 B:HIS75 4.1 92.1 1.0 CB B:ALA52 4.1 89.6 1.0 CD2 B:HIS75 4.2 93.8 1.0 CA B:CYS72 4.3 76.5 1.0 N B:HIS75 4.5 84.7 1.0 CG2 B:VAL57 4.6 67.0 1.0 CA B:CYS55 4.6 88.0 1.0 CA B:HIS75 4.7 86.0 1.0 CA B:CYS50 4.7 85.1 1.0 CB B:VAL57 4.8 80.0 1.0 C B:CYS72 4.9 75.5 1.0 C B:TYR71 5.0 73.5 1.0

P.Kloskowski, P.Neumann, P.Kumar, A.Berndt, M.Dobbelstein, R.Ficner. Myricetin-Bound Crystal Structure of the Sars-Cov-2 Helicase NSP13 Facilitates the Discovery of Novel Natural Inhibitors. Acta Crystallogr D Struct V. 81 310 2025BIOL.
ISSN: ISSN 2059-7983
PubMed: 40421686
DOI: 10.1107/S2059798325004498