Zinc in PDB 8s8x: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna)

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

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna), PDB code: 8s8x was solved by V.Kremling, J.Sprenger, D.Oberthuer, T.E.S.Scheer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.06 / 1.99
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	168.11, 168.11, 52.11, 90, 90, 120
R / Rfree (%)	18.9 / 22.3

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Toyocamycin and M7GPPPA-Rna (CAP0-Rna) (pdb code 8s8x). 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 Toyocamycin and M7GPPPA-Rna (CAP0-Rna), PDB code: 8s8x:
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 Toyocamycin and M7GPPPA-Rna (CAP0-Rna)


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 Toyocamycin and M7GPPPA-Rna (CAP0-Rna) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4401 b:51.5 occ:1.00 NE2 B:HIS4336 2.1 70.0 1.0 SG B:CYS4327 2.3 47.9 1.0 SG B:CYS4343 2.3 53.6 1.0 SG B:CYS4330 2.4 48.1 1.0 H B:CYS4330 2.9 63.6 1.0 HB2 B:CYS4343 3.0 69.5 1.0 CD2 B:HIS4336 3.0 52.7 1.0 HB3 B:CYS4327 3.1 60.6 1.0 CE1 B:HIS4336 3.1 59.0 1.0 CB B:CYS4327 3.2 50.5 1.0 HD2 B:HIS4336 3.2 63.3 1.0 HB2 B:CYS4330 3.2 53.9 1.0 CB B:CYS4343 3.3 57.8 1.0 HE1 B:HIS4336 3.3 70.9 1.0 CB B:CYS4330 3.3 44.8 1.0 HB2 B:CYS4327 3.4 60.6 1.0 N B:CYS4330 3.5 53.0 1.0 HB2 B:TYR4329 3.6 64.6 1.0 HB3 B:CYS4343 3.8 69.5 1.0 CA B:CYS4330 3.9 50.5 1.0 HA B:CYS4330 4.0 60.6 1.0 HB2 B:LYS4346 4.1 58.8 1.0 HB3 B:CYS4330 4.2 53.9 1.0 ND1 B:HIS4336 4.2 68.2 1.0 CG B:HIS4336 4.2 76.9 1.0 HB2 B:LEU4345 4.2 58.6 1.0 H B:LYS4346 4.3 59.3 1.0 HA B:CYS4343 4.3 84.6 1.0 CA B:CYS4343 4.4 70.5 1.0 HB3 B:LYS4346 4.5 58.8 1.0 HA B:ALA4324 4.5 49.5 1.0 HD2 B:TYR4329 4.5 70.1 1.0 CB B:TYR4329 4.5 53.8 1.0 CA B:CYS4327 4.6 49.8 1.0 H B:TYR4329 4.6 55.0 1.0 C B:TYR4329 4.6 56.5 1.0 H B:LEU4345 4.6 63.0 1.0 CB B:LYS4346 4.7 48.9 1.0 O B:HOH4539 4.8 65.8 1.0 HD2 B:LYS4346 4.9 69.7 1.0 C B:CYS4327 4.9 54.8 1.0 N B:LYS4346 4.9 49.3 1.0 HB3 B:TYR4329 4.9 64.6 1.0 CA B:TYR4329 5.0 58.4 1.0 HD1 B:HIS4336 5.0 81.9 1.0 HA B:CYS4327 5.0 59.8 1.0 HD12 B:LEU4345 5.0 63.1 1.0

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


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 Toyocamycin and M7GPPPA-Rna (CAP0-Rna) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:82.0 occ:1.00 SG B:CYS4370 2.3 74.1 1.0 SG B:CYS4381 2.3 86.1 1.0 SG B:CYS4373 2.4 71.0 1.0 SG B:CYS4383 2.4 90.6 1.0 HB3 B:CYS4370 3.0 88.4 1.0 H B:CYS4373 3.0 77.2 1.0 CB B:CYS4370 3.0 73.6 1.0 HB2 B:CYS4370 3.1 88.4 1.0 HB2 B:CYS4383 3.1 121.8 1.0 HB3 B:CYS4373 3.4 79.1 1.0 CB B:CYS4383 3.4 101.5 1.0 HB2 B:CYS4381 3.5 106.3 1.0 CB B:CYS4381 3.5 88.6 1.0 CB B:CYS4373 3.5 65.9 1.0 H B:CYS4383 3.6 122.2 1.0 HA B:CYS4381 3.6 112.3 1.0 HB B:VAL4372 3.7 105.6 1.0 N B:CYS4373 3.8 64.3 1.0 CA B:CYS4381 4.0 93.6 1.0 HB3 B:CYS4383 4.1 121.8 1.0 CA B:CYS4373 4.2 77.9 1.0 N B:CYS4383 4.2 101.8 1.0 H B:SER4382 4.3 115.2 1.0 HB2 B:CYS4373 4.3 79.1 1.0 HB3 B:CYS4381 4.3 106.3 1.0 H B:VAL4372 4.3 92.6 1.0 CA B:CYS4383 4.5 104.1 1.0 CA B:CYS4370 4.5 75.0 1.0 C B:CYS4381 4.5 94.7 1.0 H B:GLY4374 4.6 81.4 1.0 N B:SER4382 4.6 96.0 1.0 H B:MET4375 4.6 72.7 1.0 CB B:VAL4372 4.6 87.9 1.0 HB2 B:MET4375 4.8 70.5 1.0 HE3 B:LYS4377 4.9 115.4 1.0 HG12 B:VAL4372 4.9 89.2 1.0 HA B:CYS4383 4.9 125.0 1.0 C B:VAL4372 4.9 63.9 1.0 HA B:CYS4370 4.9 90.0 1.0 C B:CYS4373 4.9 74.5 1.0 HG3 B:LYS4377 5.0 93.5 1.0 N B:GLY4374 5.0 67.8 1.0

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