Zinc in PDB 9emj: Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Toyocamycin and M7GPPPA (CAP0-Analog)

All present enzymatic activity of Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Toyocamycin and M7GPPPA (CAP0-Analog):
2.1.1.57;

The structure of Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Toyocamycin and M7GPPPA (CAP0-Analog), PDB code: 9emj 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)	44.42 / 1.79
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.7, 168.7, 52.25, 90, 90, 120
R / Rfree (%)	18.1 / 20.7

The binding sites of Zinc atom in the Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Toyocamycin and M7GPPPA (CAP0-Analog) (pdb code 9emj). 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 Toyocamycin and M7GPPPA (CAP0-Analog), PDB code: 9emj:
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 Toyocamycin and M7GPPPA (CAP0-Analog)


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 Toyocamycin and M7GPPPA (CAP0-Analog) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:34.7 occ:1.00 NE2 B:HIS4336 2.0 43.8 1.0 SG B:CYS4327 2.3 35.0 1.0 SG B:CYS4343 2.3 36.9 1.0 SG B:CYS4330 2.3 31.9 1.0 H B:CYS4330 2.8 41.4 1.0 CE1 B:HIS4336 3.0 39.5 1.0 HB3 B:CYS4327 3.0 40.8 1.0 CD2 B:HIS4336 3.0 36.2 1.0 HB2 B:CYS4343 3.1 46.5 1.0 CB B:CYS4327 3.1 34.0 1.0 HE1 B:HIS4336 3.2 47.4 1.0 HD2 B:HIS4336 3.2 43.4 1.0 HB2 B:CYS4327 3.3 40.8 1.0 CB B:CYS4343 3.3 38.7 1.0 HB2 B:CYS4330 3.4 40.2 1.0 CB B:CYS4330 3.4 33.5 1.0 N B:CYS4330 3.5 34.5 1.0 HB2 B:TYR4329 3.6 42.5 1.0 HB3 B:CYS4343 3.9 46.5 1.0 HB2 B:LYS4346 3.9 42.8 1.0 CA B:CYS4330 3.9 33.8 1.0 HA B:CYS4330 4.1 40.6 1.0 ND1 B:HIS4336 4.1 40.0 1.0 H B:LYS4346 4.1 39.1 1.0 CG B:HIS4336 4.2 45.5 1.0 HB2 B:LEU4345 4.2 36.2 1.0 HB3 B:CYS4330 4.2 40.2 1.0 HA B:CYS4343 4.3 45.8 1.0 O B:HOH4534 4.3 43.6 1.0 CA B:CYS4343 4.5 38.1 1.0 HA B:ALA4324 4.5 32.0 1.0 CB B:TYR4329 4.5 35.5 1.0 H B:TYR4329 4.5 40.8 1.0 CA B:CYS4327 4.5 32.7 1.0 C B:TYR4329 4.5 35.2 1.0 HD2 B:TYR4329 4.6 45.7 1.0 O B:HOH4585 4.6 51.8 1.0 H B:LEU4345 4.6 37.0 1.0 HD12 B:LEU4345 4.8 43.3 1.0 CB B:LYS4346 4.9 35.7 1.0 N B:LYS4346 4.9 32.6 1.0 HD1 B:HIS4336 4.9 48.0 1.0 CA B:TYR4329 4.9 33.2 1.0 C B:CYS4327 4.9 35.5 1.0 HD2 B:LYS4346 4.9 50.3 1.0 HB3 B:TYR4329 4.9 42.5 1.0 HA B:CYS4327 4.9 39.2 1.0 N B:TYR4329 4.9 34.0 1.0 O B:CYS4327 5.0 30.0 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Toyocamycin and M7GPPPA (CAP0-Analog)


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 Toyocamycin and M7GPPPA (CAP0-Analog) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4403 b:48.4 occ:1.00 SG B:CYS4381 2.2 47.5 1.0 SG B:CYS4370 2.3 48.6 1.0 SG B:CYS4383 2.4 52.5 1.0 SG B:CYS4373 2.4 45.7 1.0 HB2 B:CYS4383 2.9 71.2 1.0 HB3 B:CYS4370 3.0 63.9 1.0 CB B:CYS4370 3.1 53.3 1.0 H B:CYS4373 3.1 50.8 1.0 HB2 B:CYS4370 3.1 63.9 1.0 HB3 B:CYS4373 3.2 55.5 1.0 CB B:CYS4383 3.2 59.3 1.0 H B:CYS4383 3.3 86.3 1.0 CB B:CYS4373 3.4 46.2 1.0 HB2 B:CYS4381 3.4 63.5 1.0 CB B:CYS4381 3.5 53.0 1.0 HB B:VAL4372 3.6 68.9 1.0 HA B:CYS4381 3.7 52.9 1.0 O B:HOH4546 3.8 52.3 1.0 N B:CYS4373 3.8 42.3 1.0 HB3 B:CYS4383 3.9 71.2 1.0 N B:CYS4383 4.0 71.9 1.0 CA B:CYS4381 4.1 44.1 1.0 H B:SER4382 4.1 60.1 1.0 HB2 B:CYS4373 4.2 55.5 1.0 CA B:CYS4373 4.2 55.0 1.0 CA B:CYS4383 4.2 73.9 1.0 HB3 B:CYS4381 4.3 63.5 1.0 HZ3 B:LYS4377 4.3 99.7 1.0 HB2 B:MET4375 4.3 49.4 1.0 O B:HOH4568 4.3 57.0 1.0 H B:VAL4372 4.4 55.0 1.0 N B:SER4382 4.5 50.1 1.0 H B:MET4375 4.5 52.1 1.0 CB B:VAL4372 4.5 57.4 1.0 CA B:CYS4370 4.5 44.5 1.0 C B:CYS4381 4.6 54.2 1.0 HA B:CYS4383 4.6 88.6 1.0 H B:GLY4374 4.8 51.8 1.0 HZ1 B:LYS4377 4.8 99.7 1.0 C B:VAL4372 4.9 45.3 1.0 HA B:CYS4370 4.9 53.5 1.0 C B:CYS4373 4.9 44.8 1.0 NZ B:LYS4377 5.0 83.1 1.0 HA B:CYS4373 5.0 66.0 1.0 HG23 B:VAL4372 5.0 63.1 1.0

V.Kremling, J.Sprenger, D.Oberthuer, H.N.Chapman, P.Middendorf, Y.Fernandez-Garcia, C.Ehrt, S.Falke, A.Kiene, B.Klopprogge, T.E.S.Scheer, M.Rarey, F.Barthels, S.Kuehn, S.Guenther. Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Natural and Drug-Like Purine Analogs For Guiding Structure-Based Drug Development To Be Published.