Zinc in PDB 8bsd: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Tubercidin

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

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

Resolution Low / High (Å)	37.54 / 1.95
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.47, 167.47, 51.51, 90, 90, 120
R / Rfree (%)	18 / 20.8

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

Chlorine

(Cl)

2 atoms

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


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 Tubercidin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:38.6 occ:1.00 NE2 B:HIS4336 2.0 54.5 1.0 SG B:CYS4343 2.3 38.1 1.0 SG B:CYS4327 2.3 37.4 1.0 SG B:CYS4330 2.3 36.8 1.0 H B:CYS4330 2.9 45.7 1.0 CE1 B:HIS4336 3.0 44.3 1.0 HB3 B:CYS4327 3.0 45.4 1.0 CD2 B:HIS4336 3.1 48.1 1.0 CB B:CYS4327 3.1 37.9 1.0 HE1 B:HIS4336 3.1 53.1 1.0 HB2 B:CYS4343 3.1 58.8 1.0 HB2 B:CYS4327 3.3 45.4 1.0 HD2 B:HIS4336 3.3 57.7 1.0 HB2 B:CYS4330 3.3 42.8 1.0 CB B:CYS4330 3.4 35.7 1.0 CB B:CYS4343 3.4 49.0 1.0 N B:CYS4330 3.5 38.1 1.0 HB2 B:TYR4329 3.6 52.1 1.0 CA B:CYS4330 3.9 35.5 1.0 HB2 B:LYS4346 3.9 54.1 1.0 HB3 B:CYS4343 3.9 58.8 1.0 HA B:CYS4330 4.1 42.5 1.0 ND1 B:HIS4336 4.1 44.3 1.0 H B:LYS4346 4.1 40.6 1.0 CG B:HIS4336 4.2 60.9 1.0 HB3 B:CYS4330 4.2 42.8 1.0 HB2 B:LEU4345 4.2 44.6 1.0 O1 B:EDO4406 4.3 65.0 1.0 HA B:CYS4343 4.3 53.3 1.0 H21 B:EDO4406 4.4 85.7 1.0 HD2 B:TYR4329 4.5 56.2 1.0 HA B:ALA4324 4.5 42.5 1.0 CA B:CYS4343 4.5 44.5 1.0 CB B:TYR4329 4.5 43.5 1.0 H B:TYR4329 4.5 43.3 1.0 CA B:CYS4327 4.5 35.5 1.0 C B:TYR4329 4.6 44.2 1.0 H B:LEU4345 4.6 45.7 1.0 HO1 B:EDO4406 4.7 78.0 1.0 HB3 B:LYS4346 4.7 54.1 1.0 CB B:LYS4346 4.7 45.1 1.0 HD1 B:HIS4336 4.9 53.1 1.0 C B:CYS4327 4.9 42.6 1.0 N B:LYS4346 4.9 33.9 1.0 CA B:TYR4329 4.9 43.1 1.0 O B:CYS4327 4.9 32.8 1.0 HA B:CYS4327 4.9 42.6 1.0 N B:TYR4329 4.9 36.1 1.0 HB3 B:TYR4329 4.9 52.1 1.0 HD12 B:LEU4345 5.0 48.6 1.0

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


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 Tubercidin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4403 b:58.4 occ:1.00 SG B:CYS4381 2.3 57.8 1.0 SG B:CYS4370 2.3 57.4 1.0 SG B:CYS4373 2.4 51.2 1.0 SG B:CYS4383 2.4 70.1 1.0 HB2 B:CYS4383 2.8 88.5 1.0 HB3 B:CYS4370 2.9 77.4 1.0 CB B:CYS4370 3.0 64.5 1.0 HB2 B:CYS4370 3.0 77.4 1.0 H B:CYS4373 3.0 60.5 1.0 HB3 B:CYS4373 3.2 65.8 1.0 CB B:CYS4383 3.2 73.8 1.0 CB B:CYS4373 3.4 54.9 1.0 H B:CYS4383 3.4 97.6 1.0 HB2 B:CYS4381 3.4 74.2 1.0 CB B:CYS4381 3.5 61.9 1.0 HB B:VAL4372 3.5 78.6 1.0 HA B:CYS4381 3.6 76.8 1.0 N B:CYS4373 3.8 50.4 1.0 HZ3 B:LYS4377 3.8 113.4 1.0 HB3 B:CYS4383 3.9 88.5 1.0 O B:HOH4541 4.0 60.0 1.0 N B:CYS4383 4.0 81.3 1.0 CA B:CYS4381 4.0 64.0 1.0 HE2 B:LYS4377 4.1 118.5 1.0 O B:HOH4573 4.1 64.7 1.0 H B:SER4382 4.1 73.8 1.0 HB2 B:CYS4373 4.2 65.8 1.0 CA B:CYS4373 4.2 58.9 1.0 CA B:CYS4383 4.2 88.5 1.0 HB3 B:CYS4381 4.3 74.2 1.0 H B:VAL4372 4.3 64.5 1.0 CA B:CYS4370 4.5 56.0 1.0 CB B:VAL4372 4.5 65.5 1.0 N B:SER4382 4.5 61.5 1.0 NZ B:LYS4377 4.5 94.5 1.0 H B:MET4375 4.5 59.8 1.0 HD3 B:LYS4377 4.5 99.4 1.0 HZ1 B:LYS4377 4.6 113.4 1.0 C B:CYS4381 4.6 69.5 1.0 HA B:CYS4383 4.6 106.2 1.0 HG12 B:VAL4372 4.7 68.7 1.0 HB2 B:MET4375 4.7 56.2 1.0 CE B:LYS4377 4.7 98.8 1.0 HA B:CYS4370 4.8 67.2 1.0 H B:GLY4374 4.8 63.3 1.0 C B:VAL4372 4.8 53.0 1.0 HA B:CYS4373 4.9 70.7 1.0 C B:CYS4373 4.9 60.1 1.0 N B:VAL4372 5.0 53.8 1.0 C B:CYS4370 5.0 57.2 1.0

V.Kremling, D.Oberthuer, J.Sprenger. Crystal Structures of Tubercidin Bound to the Active Site of the Sars-Cov-2 Methyltransferase NSP10-16 To Be Published.