Zinc in PDB 9eun: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam and M7GTP

All present enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam and M7GTP:
2.1.1.57;

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam and M7GTP, PDB code: 9eun 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)	48.99 / 2.33
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.55, 167.55, 52.05, 90, 90, 120
R / Rfree (%)	18.7 / 23.4

The binding sites of Zinc atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam and M7GTP (pdb code 9eun). 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 Sam and M7GTP, PDB code: 9eun:
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 Sam and M7GTP


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 Sam and M7GTP within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4401 b:49.4 occ:1.00 NE2 B:HIS4336 2.0 68.6 1.0 SG B:CYS4327 2.3 48.2 1.0 SG B:CYS4343 2.3 54.1 1.0 SG B:CYS4330 2.4 50.9 1.0 CE1 B:HIS4336 2.9 59.4 1.0 HE1 B:HIS4336 3.0 71.2 1.0 HB3 B:CYS4327 3.1 55.2 1.0 CB B:CYS4343 3.1 59.3 1.0 CD2 B:HIS4336 3.1 62.2 1.0 CB B:CYS4327 3.2 46.0 1.0 HB2 B:CYS4327 3.3 55.2 1.0 CB B:CYS4330 3.4 47.4 1.0 HD2 B:HIS4336 3.4 74.6 1.0 N B:CYS4330 3.6 52.3 1.0 HB2 B:TYR4329 3.7 73.2 1.0 CA B:CYS4330 4.0 57.1 1.0 ND1 B:HIS4336 4.1 62.8 1.0 HB2 B:LYS4346 4.1 53.2 1.0 CG B:HIS4336 4.2 67.1 1.0 H B:LYS4346 4.2 52.6 1.0 CA B:CYS4343 4.3 66.4 1.0 HB2 B:LEU4345 4.3 64.1 1.0 H B:LEU4345 4.4 57.1 1.0 HD2 B:TYR4329 4.4 73.2 1.0 HA B:ALA4324 4.5 49.7 1.0 H B:TYR4329 4.5 63.6 1.0 CA B:CYS4327 4.6 49.6 1.0 HB3 B:LYS4346 4.6 53.2 1.0 CB B:TYR4329 4.6 61.0 1.0 C B:TYR4329 4.7 59.5 1.0 CB B:LYS4346 4.8 44.3 1.0 HD1 B:HIS4336 4.8 75.4 1.0 N B:LYS4346 4.9 43.8 1.0 C B:CYS4327 4.9 47.4 1.0 H B:ASP4344 5.0 68.5 1.0 HA B:CYS4327 5.0 59.5 1.0 HD12 B:LEU4345 5.0 63.7 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sam and M7GTP


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 Sam and M7GTP within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:74.8 occ:1.00 SG B:CYS4381 2.3 71.0 1.0 SG B:CYS4370 2.3 72.9 1.0 SG B:CYS4383 2.4 90.8 1.0 SG B:CYS4373 2.4 69.7 1.0 HB3 B:CYS4370 3.0 89.2 1.0 H B:CYS4373 3.0 82.8 1.0 CB B:CYS4370 3.1 74.3 1.0 HB2 B:CYS4370 3.1 89.2 1.0 HB2 B:CYS4383 3.2 98.3 1.0 HB B:VAL4372 3.4 96.2 1.0 CB B:CYS4383 3.5 81.9 1.0 HB3 B:CYS4373 3.5 78.3 1.0 CB B:CYS4373 3.5 65.3 1.0 CB B:CYS4381 3.7 72.2 1.0 H B:CYS4383 3.7 107.9 1.0 N B:CYS4373 3.7 69.0 1.0 HB2 B:CYS4381 3.8 86.6 1.0 HA B:CYS4381 3.8 99.5 1.0 HB3 B:CYS4383 4.1 98.3 1.0 H B:VAL4372 4.2 90.3 1.0 CA B:CYS4373 4.2 81.2 1.0 H B:SER4382 4.3 90.5 1.0 CA B:CYS4381 4.3 82.9 1.0 HB2 B:CYS4373 4.3 78.3 1.0 N B:CYS4383 4.3 89.9 1.0 CB B:VAL4372 4.4 80.2 1.0 HB3 B:CYS4381 4.5 86.6 1.0 CA B:CYS4383 4.5 86.7 1.0 H B:MET4375 4.5 73.5 1.0 CA B:CYS4370 4.5 67.2 1.0 H B:GLY4374 4.7 75.5 1.0 N B:SER4382 4.7 75.4 1.0 C B:VAL4372 4.8 69.5 1.0 HA B:CYS4383 4.8 104.0 1.0 HB2 B:MET4375 4.9 74.2 1.0 HG23 B:VAL4372 4.9 106.6 1.0 C B:CYS4381 4.9 84.3 1.0 N B:VAL4372 4.9 75.3 1.0 CA B:VAL4372 4.9 71.0 1.0 HA B:CYS4370 4.9 80.6 1.0 C B:CYS4373 4.9 73.4 1.0 HE3 B:LYS4377 5.0 116.0 1.0 HG12 B:VAL4372 5.0 89.5 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.