Zinc in PDB 8ov4: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin

All present enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin:
2.1.1.57;

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin, PDB code: 8ov4 was solved by V.Kremling, J.Sprenger, D.Oberthuer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.73 / 1.93
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.05, 168.05, 51.71, 90, 90, 120
R / Rfree (%)	17.9 / 20.8

The binding sites of Zinc atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin (pdb code 8ov4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin, PDB code: 8ov4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:47.6 occ:1.00 NE2 B:HIS4336 2.1 65.0 1.0 SG B:CYS4343 2.2 50.4 1.0 SG B:CYS4327 2.2 46.6 1.0 SG B:CYS4330 2.3 42.5 1.0 H B:CYS4330 2.9 60.4 1.0 HB3 B:CYS4327 2.9 59.8 1.0 CB B:CYS4327 3.0 49.6 1.0 CE1 B:HIS4336 3.0 60.1 1.0 HB2 B:CYS4343 3.1 70.6 1.0 CD2 B:HIS4336 3.1 63.8 1.0 HB2 B:CYS4327 3.2 59.8 1.0 HE1 B:HIS4336 3.2 72.4 1.0 HD2 B:HIS4336 3.3 76.8 1.0 CB B:CYS4343 3.3 58.6 1.0 HB2 B:CYS4330 3.3 56.8 1.0 CB B:CYS4330 3.4 47.2 1.0 N B:CYS4330 3.5 50.2 1.0 HB2 B:TYR4329 3.6 62.7 1.0 HB2 B:LYS4346 3.8 55.6 1.0 HB3 B:CYS4343 3.9 70.6 1.0 CA B:CYS4330 3.9 45.3 1.0 H B:LYS4346 4.1 48.1 1.0 HA B:CYS4330 4.1 54.6 1.0 HA B:CYS4343 4.1 85.2 1.0 ND1 B:HIS4336 4.2 71.6 1.0 HB3 B:CYS4330 4.2 56.8 1.0 CG B:HIS4336 4.2 74.3 1.0 CA B:CYS4343 4.3 70.8 1.0 O B:HOH4540 4.4 63.4 1.0 HD2 B:TYR4329 4.4 72.0 1.0 HB2 B:LEU4345 4.4 54.6 1.0 H B:LEU4345 4.5 61.5 1.0 CA B:CYS4327 4.5 50.2 1.0 CB B:TYR4329 4.5 52.0 1.0 HA B:ALA4324 4.5 45.1 1.0 C B:TYR4329 4.6 52.6 1.0 H B:TYR4329 4.6 52.0 1.0 CB B:LYS4346 4.7 46.2 1.0 N B:LYS4346 4.8 39.9 1.0 HB3 B:LYS4346 4.8 55.6 1.0 HA B:CYS4327 4.9 60.5 1.0 C B:CYS4327 4.9 45.0 1.0 O B:HOH4550 4.9 66.2 1.0 CA B:TYR4329 4.9 49.3 1.0 HD1 B:HIS4336 4.9 86.2 1.0 N B:TYR4329 4.9 43.1 1.0 H B:ASP4344 5.0 79.0 1.0 O B:CYS4327 5.0 42.2 1.0 HB3 B:TYR4329 5.0 62.7 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4403 b:68.7 occ:1.00 SG B:CYS4370 2.3 67.1 1.0 SG B:CYS4381 2.3 68.5 1.0 SG B:CYS4373 2.4 62.3 1.0 SG B:CYS4383 2.4 82.7 1.0 HB2 B:CYS4383 2.9 109.0 1.0 HB3 B:CYS4370 2.9 82.5 1.0 CB B:CYS4370 3.0 68.6 1.0 HB2 B:CYS4370 3.0 82.5 1.0 H B:CYS4373 3.1 77.6 1.0 CB B:CYS4383 3.2 90.6 1.0 H B:CYS4383 3.3 106.3 1.0 HB3 B:CYS4373 3.3 69.0 1.0 HB2 B:CYS4381 3.4 86.7 1.0 CB B:CYS4381 3.5 72.0 1.0 CB B:CYS4373 3.5 57.3 1.0 O B:HOH4534 3.5 67.5 1.0 HA B:CYS4381 3.6 87.7 1.0 HB B:VAL4372 3.7 91.5 1.0 N B:CYS4373 3.8 64.5 1.0 HB3 B:CYS4383 3.9 109.0 1.0 N B:CYS4383 4.0 88.4 1.0 CA B:CYS4381 4.0 73.0 1.0 HZ2 B:LYS4377 4.0 121.5 1.0 H B:SER4382 4.1 83.4 1.0 HD3 B:LYS4377 4.2 105.8 1.0 CA B:CYS4383 4.2 91.3 1.0 HB2 B:CYS4373 4.2 69.0 1.0 CA B:CYS4373 4.3 68.4 1.0 HB3 B:CYS4381 4.3 86.7 1.0 H B:VAL4372 4.3 75.2 1.0 CA B:CYS4370 4.4 66.6 1.0 N B:SER4382 4.5 69.4 1.0 HB2 B:MET4375 4.5 60.6 1.0 C B:CYS4381 4.6 71.1 1.0 H B:MET4375 4.6 67.4 1.0 CB B:VAL4372 4.6 76.1 1.0 HA B:CYS4383 4.7 109.8 1.0 HD2 B:LYS4377 4.7 105.8 1.0 H B:GLY4374 4.7 78.8 1.0 HA B:CYS4370 4.8 80.2 1.0 NZ B:LYS4377 4.8 101.0 1.0 CD B:LYS4377 4.9 88.0 1.0 C B:VAL4372 4.9 67.1 1.0 C B:CYS4370 4.9 65.0 1.0 HZ3 B:LYS4377 4.9 121.5 1.0 N B:VAL4372 5.0 62.5 1.0

V.Kremling, D.Oberthuer, O.Yefanov, M.Galchenkova, P.Middendorf, Y.Fernandez Garcia, C.Ehrt, S.Falke, A.Kiene, B.Klopprogge, H.Chapman, J.Sprenger. Crystal Structures of Tubercidin and Adenosine Bound to the Active Site of Thesars-Cov-2 Methyltransferase NSP10-16 To Be Published.