Zinc in PDB 9emv: Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sangivamycin and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog)

All present enzymatic activity of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sangivamycin and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog):
2.1.1.57;

The structure of Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sangivamycin and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog), PDB code: 9emv 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)	44.48 / 2.34
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.51, 169.51, 52.25, 90, 90, 120
R / Rfree (%)	20.3 / 25.6

The binding sites of Zinc atom in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sangivamycin and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog) (pdb code 9emv). 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 (CAP0-Analog)/M7GPPPAM (CAP1-Analog), PDB code: 9emv:
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 (CAP0-Analog)/M7GPPPAM (CAP1-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 NSP10-16 Methyltransferase in Complex with Sangivamycin and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4401 b:53.7 occ:1.00 NE2 B:HIS4336 2.1 68.1 1.0 SG B:CYS4327 2.3 47.4 1.0 SG B:CYS4330 2.3 58.8 1.0 SG B:CYS4343 2.3 56.3 1.0 H B:CYS4330 2.9 73.5 1.0 CE1 B:HIS4336 3.0 62.2 1.0 CD2 B:HIS4336 3.1 72.3 1.0 HE1 B:HIS4336 3.2 74.7 1.0 HB2 B:CYS4343 3.2 90.9 1.0 HB3 B:CYS4327 3.2 73.0 1.0 HD2 B:HIS4336 3.3 86.8 1.0 CB B:CYS4327 3.3 60.9 1.0 CB B:CYS4343 3.4 75.7 1.0 N B:CYS4330 3.5 61.2 1.0 HB2 B:TYR4329 3.5 81.1 1.0 CB B:CYS4330 3.5 59.8 1.0 HB2 B:CYS4327 3.6 73.0 1.0 HB2 B:CYS4330 3.7 71.8 1.0 CA B:CYS4330 3.9 68.0 1.0 HB3 B:CYS4343 4.0 90.9 1.0 HA B:CYS4330 4.1 81.7 1.0 HB2 B:LYS4346 4.1 57.0 1.0 ND1 B:HIS4336 4.1 74.4 1.0 CG B:HIS4336 4.2 75.6 1.0 H B:LYS4346 4.2 60.0 1.0 HA B:CYS4343 4.2 88.0 1.0 HB3 B:CYS4330 4.3 71.8 1.0 HB2 B:LEU4345 4.3 60.0 1.0 CB B:TYR4329 4.4 67.5 1.0 C B:TYR4329 4.4 71.2 1.0 H B:TYR4329 4.4 65.8 1.0 CA B:CYS4343 4.5 73.4 1.0 HA B:ALA4324 4.6 64.4 1.0 H B:LEU4345 4.6 75.6 1.0 CA B:CYS4327 4.7 62.0 1.0 HB3 B:TYR4329 4.7 81.1 1.0 HD2 B:TYR4329 4.7 80.7 1.0 CA B:TYR4329 4.7 62.4 1.0 HB3 B:LYS4346 4.8 57.0 1.0 N B:TYR4329 4.8 54.8 1.0 O B:CYS4327 4.8 55.7 1.0 C B:CYS4327 4.9 56.9 1.0 CB B:LYS4346 4.9 47.5 1.0 HD1 B:HIS4336 4.9 89.3 1.0 N B:LYS4346 5.0 50.0 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 NSP10-16 Methyltransferase in Complex with Sangivamycin and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-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 NSP10-16 Methyltransferase in Complex with Sangivamycin and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:73.7 occ:1.00 SG B:CYS4381 2.2 53.5 1.0 SG B:CYS4370 2.3 64.9 1.0 SG B:CYS4373 2.3 76.3 1.0 SG B:CYS4383 2.4 76.9 1.0 H B:CYS4373 2.8 79.9 1.0 HB2 B:CYS4383 2.9 84.2 1.0 HB3 B:CYS4370 3.0 102.3 1.0 CB B:CYS4370 3.1 85.2 1.0 HB2 B:CYS4370 3.1 102.3 1.0 HB3 B:CYS4373 3.3 88.1 1.0 CB B:CYS4383 3.3 70.2 1.0 CB B:CYS4373 3.4 73.5 1.0 HB2 B:CYS4381 3.4 96.2 1.0 H B:CYS4383 3.4 119.3 1.0 CB B:CYS4381 3.4 80.2 1.0 HB B:VAL4372 3.5 108.2 1.0 N B:CYS4373 3.5 66.6 1.0 HA B:CYS4381 3.5 86.7 1.0 HB3 B:CYS4383 4.0 84.2 1.0 CA B:CYS4381 4.0 72.3 1.0 CA B:CYS4373 4.0 81.6 1.0 N B:CYS4383 4.1 99.5 1.0 HB2 B:CYS4373 4.2 88.1 1.0 HB3 B:CYS4381 4.2 96.2 1.0 H B:VAL4372 4.2 82.5 1.0 CA B:CYS4383 4.3 102.3 1.0 CB B:VAL4372 4.4 90.2 1.0 HG12 B:VAL4372 4.4 73.0 1.0 H B:SER4382 4.4 93.0 1.0 H B:GLY4374 4.5 74.0 1.0 H B:MET4375 4.5 83.5 1.0 CA B:CYS4370 4.5 76.2 1.0 C B:CYS4381 4.6 77.4 1.0 HA B:CYS4383 4.6 122.8 1.0 C B:VAL4372 4.6 74.1 1.0 N B:SER4382 4.7 77.5 1.0 HB2 B:MET4375 4.8 68.0 1.0 C B:CYS4373 4.8 73.8 1.0 HA B:CYS4373 4.8 97.9 1.0 HA B:CYS4370 4.9 91.5 1.0 N B:GLY4374 4.9 61.7 1.0 N B:VAL4372 4.9 68.7 1.0 CA B:VAL4372 4.9 81.4 1.0 CG1 B:VAL4372 4.9 60.8 1.0 HG3 B:LYS4377 5.0 103.9 1.0

V.Kremling, S.Falke, Y.Fernandez-Garcia, C.Ehrt, A.Kiene, B.Klopprogge, E.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.