Zinc in PDB 8s8w: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sangivamycin and M7GPPPA-Rna (CAP0-Rna)

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

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sangivamycin and M7GPPPA-Rna (CAP0-Rna), PDB code: 8s8w 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)	48.80 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.14, 167.14, 51.83, 90, 90, 120
R / Rfree (%)	18.7 / 22.4

The binding sites of Zinc atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sangivamycin and M7GPPPA-Rna (CAP0-Rna) (pdb code 8s8w). 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 Sangivamycin and M7GPPPA-Rna (CAP0-Rna), PDB code: 8s8w:
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 Sangivamycin 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 Sangivamycin and M7GPPPA-Rna (CAP0-Rna) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4401 b:51.9 occ:1.00 NE2 B:HIS4336 2.0 65.8 1.0 SG B:CYS4327 2.3 48.2 1.0 SG B:CYS4343 2.3 53.2 1.0 SG B:CYS4330 2.3 48.0 1.0 H B:CYS4330 2.9 60.1 1.0 HB2 B:CYS4343 2.9 69.4 1.0 CE1 B:HIS4336 3.0 61.5 1.0 CD2 B:HIS4336 3.1 51.9 1.0 HB3 B:CYS4327 3.1 58.1 1.0 HE1 B:HIS4336 3.1 74.0 1.0 CB B:CYS4327 3.2 48.4 1.0 CB B:CYS4343 3.2 57.8 1.0 HD2 B:HIS4336 3.3 62.4 1.0 HB2 B:CYS4330 3.3 55.9 1.0 HB2 B:CYS4327 3.3 58.1 1.0 CB B:CYS4330 3.4 46.5 1.0 N B:CYS4330 3.6 50.0 1.0 HB2 B:TYR4329 3.6 75.9 1.0 HB3 B:CYS4343 3.8 69.4 1.0 CA B:CYS4330 4.0 53.2 1.0 ND1 B:HIS4336 4.1 63.3 1.0 HB2 B:LYS4346 4.2 55.6 1.0 HA B:CYS4330 4.2 63.9 1.0 HA B:CYS4343 4.2 74.6 1.0 CG B:HIS4336 4.2 70.4 1.0 HB3 B:CYS4330 4.2 55.9 1.0 H B:LYS4346 4.3 54.9 1.0 HD2 B:TYR4329 4.3 73.9 1.0 CA B:CYS4343 4.3 62.1 1.0 HB2 B:LEU4345 4.4 56.5 1.0 H B:TYR4329 4.5 56.1 1.0 HA B:ALA4324 4.5 42.2 1.0 H B:LEU4345 4.5 53.0 1.0 CB B:TYR4329 4.6 63.1 1.0 CA B:CYS4327 4.6 46.8 1.0 HB3 B:LYS4346 4.6 55.6 1.0 C B:TYR4329 4.6 61.8 1.0 CB B:LYS4346 4.8 46.2 1.0 HD1 B:HIS4336 4.9 76.0 1.0 C B:CYS4327 4.9 50.8 1.0 N B:TYR4329 5.0 46.7 1.0 N B:LYS4346 5.0 45.7 1.0 HA B:CYS4327 5.0 56.2 1.0 O B:CYS4327 5.0 45.6 1.0 CA B:TYR4329 5.0 57.7 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sangivamycin 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 Sangivamycin and M7GPPPA-Rna (CAP0-Rna) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:83.7 occ:1.00 SG B:CYS4370 2.3 75.2 1.0 SG B:CYS4381 2.3 78.6 1.0 SG B:CYS4373 2.4 73.2 1.0 SG B:CYS4383 2.4 95.6 1.0 HB3 B:CYS4370 2.9 84.4 1.0 CB B:CYS4370 3.0 70.3 1.0 HB2 B:CYS4370 3.1 84.4 1.0 H B:CYS4373 3.1 82.3 1.0 HB2 B:CYS4383 3.2 109.8 1.0 HB3 B:CYS4373 3.3 81.9 1.0 CB B:CYS4383 3.4 91.4 1.0 CB B:CYS4373 3.4 68.1 1.0 HB B:VAL4372 3.6 97.5 1.0 CB B:CYS4381 3.6 78.0 1.0 HB2 B:CYS4381 3.6 93.7 1.0 H B:CYS4383 3.7 116.9 1.0 HA B:CYS4381 3.7 105.9 1.0 N B:CYS4373 3.8 68.5 1.0 HB3 B:CYS4383 4.1 109.8 1.0 H B:SER4382 4.1 107.5 1.0 CA B:CYS4381 4.1 88.2 1.0 CA B:CYS4373 4.2 76.4 1.0 HB2 B:CYS4373 4.2 81.9 1.0 N B:CYS4383 4.3 97.3 1.0 H B:VAL4372 4.3 84.8 1.0 HB3 B:CYS4381 4.4 93.7 1.0 HE2 B:LYS4377 4.5 118.2 1.0 H B:MET4375 4.5 75.8 1.0 CA B:CYS4370 4.5 71.5 1.0 CB B:VAL4372 4.5 81.1 1.0 CA B:CYS4383 4.5 93.5 1.0 N B:SER4382 4.6 89.5 1.0 H B:GLY4374 4.6 72.6 1.0 C B:CYS4381 4.7 92.9 1.0 C B:VAL4372 4.9 67.3 1.0 C B:CYS4373 4.9 76.7 1.0 HB2 B:MET4375 4.9 85.7 1.0 HA B:CYS4370 4.9 85.9 1.0 C B:CYS4370 4.9 66.8 1.0 O B:CYS4370 4.9 78.2 1.0 N B:GLY4374 5.0 60.5 1.0 N B:VAL4372 5.0 70.6 1.0 HA B:CYS4383 5.0 112.2 1.0

V.Kremling, S.Falke, Y.Fernandez-Garcia, C.Ehrt, K.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.