Zinc in PDB 9gny: Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Caffeine

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

The structure of Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Caffeine, PDB code: 9gny was solved by V.Kremling, J.Sprenger, D.Oberthuer, A.Kiene, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.47 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.04, 167.04, 51.44, 90, 90, 120
R / Rfree (%)	19 / 21.2

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

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and Caffeine (pdb code 9gny). 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 Methyltransferase NSP10-16 in Complex with Sam and Caffeine, PDB code: 9gny:
Jump to Zinc binding site number: 1; 2;

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


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 Methyltransferase NSP10-16 in Complex with Sam and Caffeine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:37.1 occ:1.00 NE2 B:HIS4336 2.0 45.1 1.0 SG B:CYS4327 2.3 36.0 1.0 SG B:CYS4343 2.3 36.9 1.0 SG B:CYS4330 2.3 37.2 1.0 H B:CYS4330 3.0 42.4 1.0 HB2 B:CYS4343 3.0 54.7 1.0 CE1 B:HIS4336 3.0 43.5 1.0 CD2 B:HIS4336 3.0 41.5 1.0 HB3 B:CYS4327 3.0 49.8 1.0 CB B:CYS4327 3.1 41.5 1.0 HE1 B:HIS4336 3.2 52.2 1.0 HD2 B:HIS4336 3.2 49.8 1.0 CB B:CYS4343 3.2 45.6 1.0 HB2 B:CYS4327 3.3 49.8 1.0 HB2 B:CYS4330 3.4 39.5 1.0 CB B:CYS4330 3.4 32.9 1.0 N B:CYS4330 3.6 35.3 1.0 HB2 B:TYR4329 3.6 50.6 1.0 HB3 B:CYS4343 3.8 54.7 1.0 CA B:CYS4330 4.0 35.5 1.0 HB2 B:LYS4346 4.0 45.0 1.0 ND1 B:HIS4336 4.1 46.1 1.0 CG B:HIS4336 4.1 48.9 1.0 HA B:CYS4330 4.2 42.6 1.0 HA B:CYS4343 4.3 59.3 1.0 HB3 B:CYS4330 4.3 39.5 1.0 O B:HOH4582 4.3 51.2 1.0 H B:LYS4346 4.4 42.9 1.0 CA B:CYS4343 4.4 49.4 1.0 HD2 B:TYR4329 4.4 47.0 1.0 HB2 B:LEU4345 4.5 48.0 1.0 HA B:ALA4324 4.5 35.8 1.0 CA B:CYS4327 4.6 35.6 1.0 H B:TYR4329 4.6 41.3 1.0 CB B:TYR4329 4.6 42.2 1.0 H B:LEU4345 4.6 45.3 1.0 C B:TYR4329 4.6 38.8 1.0 CB B:LYS4346 4.9 37.5 1.0 HB3 B:LYS4346 4.9 45.0 1.0 HD1 B:HIS4336 4.9 55.3 1.0 C B:CYS4327 4.9 35.3 1.0 HA B:CYS4327 4.9 42.7 1.0 HD12 B:LEU4345 5.0 50.2 1.0 CA B:TYR4329 5.0 37.1 1.0 N B:TYR4329 5.0 34.4 1.0

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


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 Methyltransferase NSP10-16 in Complex with Sam and Caffeine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4403 b:56.9 occ:1.00 SG B:CYS4370 2.3 53.2 1.0 SG B:CYS4381 2.3 55.1 1.0 SG B:CYS4373 2.4 50.7 1.0 SG B:CYS4383 2.4 67.2 1.0 HB2 B:CYS4383 2.9 84.7 1.0 HB3 B:CYS4373 3.0 61.2 1.0 HB3 B:CYS4370 3.0 70.4 1.0 CB B:CYS4370 3.0 58.7 1.0 H B:CYS4373 3.1 63.1 1.0 HB2 B:CYS4370 3.1 70.4 1.0 CB B:CYS4383 3.2 70.6 1.0 CB B:CYS4373 3.2 51.0 1.0 H B:CYS4383 3.4 88.3 1.0 HB2 B:CYS4381 3.4 67.8 1.0 CB B:CYS4381 3.5 56.5 1.0 HZ3 B:LYS4377 3.6 113.0 1.0 HA B:CYS4381 3.6 70.1 1.0 HB B:VAL4372 3.6 68.8 1.0 N B:CYS4373 3.7 52.6 1.0 O B:HOH4535 3.9 54.0 1.0 HB3 B:CYS4383 3.9 84.7 1.0 HB2 B:CYS4373 4.0 61.2 1.0 N B:CYS4383 4.0 73.6 1.0 CA B:CYS4381 4.0 58.5 1.0 H B:SER4382 4.1 75.1 1.0 CA B:CYS4373 4.1 52.8 1.0 CA B:CYS4383 4.2 76.7 1.0 HB3 B:CYS4381 4.3 67.8 1.0 NZ B:LYS4377 4.3 94.2 1.0 HE2 B:LYS4377 4.4 106.6 1.0 H B:VAL4372 4.4 62.7 1.0 HD3 B:LYS4377 4.4 89.0 1.0 HZ1 B:LYS4377 4.4 113.0 1.0 N B:SER4382 4.4 62.5 1.0 HG12 B:VAL4372 4.5 61.4 1.0 H B:MET4375 4.5 58.9 1.0 CA B:CYS4370 4.5 54.5 1.0 C B:CYS4381 4.6 62.3 1.0 CB B:VAL4372 4.6 57.3 1.0 HB2 B:MET4375 4.6 56.6 1.0 HA B:CYS4383 4.7 92.0 1.0 H B:GLY4374 4.7 61.0 1.0 CE B:LYS4377 4.8 88.8 1.0 C B:VAL4372 4.8 48.3 1.0 HA B:CYS4373 4.9 63.4 1.0 HA B:CYS4370 4.9 65.4 1.0 C B:CYS4373 4.9 56.7 1.0

V.Kremling, J.Sprenger, D.Oberthuer, H.N.Chapman, P.Middendorf, S.Falke, A.Kiene, B.Klopprogge, T.E.S.Scheer, A.Creon. Crystal Structures of Sars-Cov-2 Methyltransferase NSP10-16 with CAP0-Site Binders To Be Published.