Zinc in PDB 8bzv: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adenosine

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

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Adenosine, PDB code: 8bzv 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)	42.00 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.32, 167.32, 51.54, 90, 90, 120
R / Rfree (%)	17.8 / 20

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

Chlorine

(Cl)

1 atom

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


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:31.6 occ:1.00 NE2 B:HIS4336 2.1 37.5 1.0 SG B:CYS4343 2.3 32.1 1.0 SG B:CYS4327 2.3 30.5 1.0 SG B:CYS4330 2.3 30.4 1.0 H B:CYS4330 2.9 36.7 1.0 CE1 B:HIS4336 3.0 37.8 1.0 HB2 B:CYS4343 3.0 47.4 1.0 CD2 B:HIS4336 3.1 36.9 1.0 HB3 B:CYS4327 3.1 41.5 1.0 CB B:CYS4327 3.2 34.6 1.0 HE1 B:HIS4336 3.2 45.2 1.0 HD2 B:HIS4336 3.2 44.2 1.0 CB B:CYS4343 3.3 39.5 1.0 HB2 B:CYS4330 3.4 33.7 1.0 HB2 B:CYS4327 3.4 41.5 1.0 CB B:CYS4330 3.4 28.1 1.0 N B:CYS4330 3.6 30.6 1.0 HB2 B:TYR4329 3.6 42.7 1.0 HB3 B:CYS4343 3.9 47.4 1.0 HB2 B:LYS4346 3.9 38.4 1.0 H22 B:EDO4408 4.0 73.0 1.0 CA B:CYS4330 4.0 25.4 1.0 HO2 B:EDO4408 4.1 58.5 1.0 ND1 B:HIS4336 4.1 33.6 1.0 HA B:CYS4330 4.2 30.5 1.0 CG B:HIS4336 4.2 46.0 1.0 H B:LYS4346 4.2 34.1 1.0 HB3 B:CYS4330 4.2 33.7 1.0 HA B:CYS4343 4.3 49.8 1.0 O2 B:EDO4408 4.3 48.8 1.0 HB2 B:LEU4345 4.4 36.8 1.0 CA B:CYS4343 4.4 41.5 1.0 HA B:ALA4324 4.5 30.3 1.0 HD2 B:TYR4329 4.5 44.0 1.0 H B:TYR4329 4.6 37.5 1.0 CB B:TYR4329 4.6 35.7 1.0 H B:LEU4345 4.6 41.4 1.0 CA B:CYS4327 4.6 29.1 1.0 C B:TYR4329 4.6 31.5 1.0 C2 B:EDO4408 4.7 60.9 1.0 CB B:LYS4346 4.8 32.1 1.0 HB3 B:LYS4346 4.8 38.4 1.0 HD1 B:HIS4336 4.9 40.2 1.0 N B:LYS4346 4.9 28.5 1.0 CA B:TYR4329 5.0 31.0 1.0 C B:CYS4327 5.0 30.4 1.0 N B:TYR4329 5.0 31.3 1.0 HB3 B:TYR4329 5.0 42.7 1.0

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


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 Adenosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4403 b:53.3 occ:1.00 SG B:CYS4381 2.3 52.9 1.0 SG B:CYS4370 2.3 54.0 1.0 SG B:CYS4373 2.4 47.8 1.0 SG B:CYS4383 2.4 63.0 1.0 HB3 B:CYS4370 2.9 61.5 1.0 HB2 B:CYS4383 3.0 77.5 1.0 CB B:CYS4370 3.0 51.3 1.0 H B:CYS4373 3.0 58.9 1.0 HB2 B:CYS4370 3.0 61.5 1.0 HB3 B:CYS4373 3.3 55.2 1.0 CB B:CYS4383 3.3 64.6 1.0 CB B:CYS4373 3.4 46.0 1.0 HB2 B:CYS4381 3.5 62.6 1.0 HB B:VAL4372 3.5 77.0 1.0 CB B:CYS4381 3.5 52.2 1.0 H B:CYS4383 3.6 87.9 1.0 HZ3 B:LYS4377 3.7 110.2 1.0 N B:CYS4373 3.7 49.2 1.0 HA B:CYS4381 3.7 71.3 1.0 HB3 B:CYS4383 4.0 77.5 1.0 O B:HOH4544 4.1 54.5 1.0 H B:SER4382 4.1 73.4 1.0 CA B:CYS4381 4.1 59.5 1.0 CA B:CYS4373 4.2 46.8 1.0 N B:CYS4383 4.2 73.3 1.0 HB2 B:CYS4373 4.2 55.2 1.0 O B:HOH4582 4.2 59.1 1.0 H B:VAL4372 4.3 68.5 1.0 HB3 B:CYS4381 4.3 62.6 1.0 HE2 B:LYS4377 4.3 104.9 1.0 CA B:CYS4383 4.4 75.6 1.0 NZ B:LYS4377 4.4 91.9 1.0 HZ1 B:LYS4377 4.4 110.2 1.0 H B:MET4375 4.5 50.1 1.0 CB B:VAL4372 4.5 64.2 1.0 CA B:CYS4370 4.5 52.1 1.0 N B:SER4382 4.5 61.2 1.0 H B:GLY4374 4.7 55.0 1.0 C B:CYS4381 4.7 64.2 1.0 HD3 B:LYS4377 4.7 89.4 1.0 HA B:CYS4383 4.7 90.6 1.0 C B:VAL4372 4.8 45.1 1.0 HA B:CYS4370 4.8 62.4 1.0 HB2 B:MET4375 4.8 55.5 1.0 HG12 B:VAL4372 4.8 66.9 1.0 CE B:LYS4377 4.8 87.5 1.0 C B:CYS4373 4.9 48.7 1.0 HA B:CYS4373 4.9 56.1 1.0 N B:VAL4372 4.9 57.1 1.0 CA B:VAL4372 5.0 55.1 1.0 C B:CYS4370 5.0 51.8 1.0

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