Zinc in PDB 8ov3: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with 5-Iodotubercidin

All present enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with 5-Iodotubercidin:
2.1.1.57;

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with 5-Iodotubercidin, PDB code: 8ov3 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)	48.21 / 1.82
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.01, 167.01, 51.4, 90, 90, 120
R / Rfree (%)	18.2 / 21.1

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with 5-Iodotubercidin also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Zinc atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with 5-Iodotubercidin (pdb code 8ov3). 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 5-Iodotubercidin, PDB code: 8ov3:
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 5-Iodotubercidin


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 5-Iodotubercidin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:41.0 occ:1.00 NE2 B:HIS4336 2.1 50.5 1.0 SG B:CYS4343 2.2 45.9 1.0 SG B:CYS4327 2.3 39.6 1.0 SG B:CYS4330 2.3 38.2 1.0 H B:CYS4330 3.0 44.8 1.0 HB2 B:CYS4343 3.0 61.1 1.0 HB3 B:CYS4327 3.0 48.0 1.0 CE1 B:HIS4336 3.0 47.7 1.0 CD2 B:HIS4336 3.1 50.9 1.0 CB B:CYS4327 3.1 40.0 1.0 HE1 B:HIS4336 3.2 57.2 1.0 CB B:CYS4343 3.2 50.9 1.0 HD2 B:HIS4336 3.3 61.1 1.0 HB2 B:CYS4327 3.3 48.0 1.0 HB2 B:CYS4330 3.3 45.5 1.0 CB B:CYS4330 3.4 37.9 1.0 HB2 B:TYR4329 3.5 53.2 1.0 N B:CYS4330 3.6 37.3 1.0 HB2 B:LYS4346 3.8 43.2 1.0 HB3 B:CYS4343 3.8 61.1 1.0 CA B:CYS4330 4.0 37.6 1.0 H B:LYS4346 4.1 42.4 1.0 HA B:CYS4330 4.1 45.2 1.0 ND1 B:HIS4336 4.1 49.9 1.0 HA B:CYS4343 4.2 82.4 1.0 CG B:HIS4336 4.2 63.8 1.0 HB3 B:CYS4330 4.2 45.5 1.0 CA B:CYS4343 4.3 68.7 1.0 HB2 B:LEU4345 4.4 44.5 1.0 HD2 B:TYR4329 4.4 62.6 1.0 H B:LEU4345 4.4 52.4 1.0 CB B:TYR4329 4.5 44.4 1.0 HA B:ALA4324 4.5 38.9 1.0 H B:TYR4329 4.5 43.8 1.0 CA B:CYS4327 4.5 37.9 1.0 C B:TYR4329 4.6 45.2 1.0 CB B:LYS4346 4.7 36.0 1.0 HB3 B:LYS4346 4.8 43.2 1.0 N B:LYS4346 4.9 35.3 1.0 HB3 B:TYR4329 4.9 53.2 1.0 CA B:TYR4329 4.9 42.3 1.0 C B:CYS4327 4.9 39.6 1.0 HD1 B:HIS4336 4.9 60.0 1.0 HA B:CYS4327 4.9 45.5 1.0 N B:TYR4329 4.9 36.5 1.0 O B:CYS4327 5.0 37.0 1.0 H B:ASP4344 5.0 70.6 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with 5-Iodotubercidin


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 5-Iodotubercidin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4403 b:59.2 occ:1.00 SG B:CYS4370 2.3 58.2 1.0 SG B:CYS4381 2.3 60.9 1.0 SG B:CYS4373 2.4 53.0 1.0 SG B:CYS4383 2.4 72.1 1.0 HB2 B:CYS4383 2.9 92.6 1.0 HB3 B:CYS4370 2.9 74.2 1.0 H B:CYS4373 3.0 74.1 1.0 CB B:CYS4370 3.0 61.8 1.0 HB2 B:CYS4370 3.0 74.2 1.0 HB3 B:CYS4373 3.1 64.4 1.0 CB B:CYS4383 3.2 77.1 1.0 CB B:CYS4373 3.3 53.6 1.0 HB2 B:CYS4381 3.5 79.9 1.0 CB B:CYS4381 3.5 66.5 1.0 HA B:CYS4381 3.6 84.7 1.0 N B:CYS4373 3.7 61.7 1.0 HB B:VAL4372 3.8 80.7 1.0 H B:CYS4383 3.8 100.1 1.0 HB3 B:CYS4383 3.8 92.6 1.0 O B:HOH4532 4.1 58.8 1.0 CA B:CYS4381 4.1 70.5 1.0 CA B:CYS4373 4.1 63.7 1.0 HB2 B:CYS4373 4.1 64.4 1.0 HZ2 B:LYS4377 4.1 107.8 1.0 H B:SER4382 4.2 84.8 1.0 HD3 B:LYS4377 4.3 90.0 1.0 HZ3 B:LYS4377 4.3 107.8 1.0 O B:HOH4555 4.3 62.3 1.0 N B:CYS4383 4.3 83.4 1.0 H B:VAL4372 4.3 69.7 1.0 HB3 B:CYS4381 4.3 79.9 1.0 CA B:CYS4383 4.4 82.2 1.0 H B:MET4375 4.4 64.8 1.0 HB2 B:MET4375 4.5 65.4 1.0 CA B:CYS4370 4.5 57.5 1.0 N B:SER4382 4.6 70.6 1.0 NZ B:LYS4377 4.6 89.8 1.0 C B:CYS4381 4.6 72.3 1.0 H B:GLY4374 4.7 60.8 1.0 CB B:VAL4372 4.7 67.2 1.0 HA B:CYS4383 4.7 98.7 1.0 C B:VAL4372 4.8 56.8 1.0 HA B:CYS4370 4.8 69.1 1.0 HA B:CYS4373 4.9 76.4 1.0 C B:CYS4373 4.9 60.6 1.0 C B:CYS4370 5.0 61.6 1.0

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