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

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

The structure of Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog), PDB code: 9eml 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)	49.07 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	167.74, 167.74, 52.13, 90, 90, 120
R / Rfree (%)	17.8 / 24

The binding sites of Zinc atom in the Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog) (pdb code 9eml). 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 Sam and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog), PDB code: 9eml:
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 Sam 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 Methyltransferase NSP10-16 in Complex with Sam and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4401 b:47.9 occ:1.00 NE2 B:HIS4336 2.0 68.7 1.0 SG B:CYS4327 2.3 46.2 1.0 SG B:CYS4330 2.3 47.9 1.0 SG B:CYS4343 2.3 47.0 1.0 H B:CYS4330 2.8 56.6 1.0 CE1 B:HIS4336 2.8 58.8 1.0 HE1 B:HIS4336 2.9 70.4 1.0 HB2 B:CYS4343 3.0 61.6 1.0 HB3 B:CYS4327 3.1 54.5 1.0 CB B:CYS4327 3.2 45.5 1.0 CD2 B:HIS4336 3.2 56.6 1.0 HB2 B:CYS4330 3.2 47.2 1.0 CB B:CYS4343 3.3 51.5 1.0 CB B:CYS4330 3.3 39.5 1.0 HB2 B:CYS4327 3.3 54.5 1.0 N B:CYS4330 3.5 47.3 1.0 HD2 B:HIS4336 3.5 67.8 1.0 HB2 B:TYR4329 3.6 68.4 1.0 HB3 B:CYS4343 3.8 61.6 1.0 CA B:CYS4330 3.9 51.7 1.0 ND1 B:HIS4336 4.0 52.1 1.0 HA B:CYS4330 4.1 61.8 1.0 HB3 B:CYS4330 4.1 47.2 1.0 CG B:HIS4336 4.2 68.5 1.0 H B:LYS4346 4.3 55.2 1.0 HB2 B:LYS4346 4.3 48.8 1.0 HB2 B:LEU4345 4.3 66.0 1.0 HA B:CYS4343 4.4 68.9 1.0 H B:TYR4329 4.4 50.5 1.0 HB3 B:LYS4346 4.5 48.8 1.0 CA B:CYS4343 4.5 57.5 1.0 HD2 B:TYR4329 4.5 67.8 1.0 HA B:ALA4324 4.5 52.8 1.0 CB B:TYR4329 4.5 57.1 1.0 C B:TYR4329 4.6 51.3 1.0 H B:LEU4345 4.6 59.0 1.0 CA B:CYS4327 4.6 43.9 1.0 HD12 B:LEU4345 4.7 76.3 1.0 HD1 B:HIS4336 4.8 62.3 1.0 CB B:LYS4346 4.8 40.8 1.0 N B:TYR4329 4.9 42.2 1.0 C B:CYS4327 4.9 48.3 1.0 CA B:TYR4329 4.9 46.7 1.0 N B:LYS4346 5.0 46.2 1.0 HB3 B:TYR4329 5.0 68.4 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 Methyltransferase NSP10-16 in Complex with Sam 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 Methyltransferase NSP10-16 in Complex with Sam and M7GPPPA (CAP0-Analog)/M7GPPPAM (CAP1-Analog) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:75.3 occ:1.00 SG B:CYS4370 2.3 73.2 1.0 SG B:CYS4383 2.3 87.5 1.0 SG B:CYS4381 2.3 76.2 1.0 SG B:CYS4373 2.4 66.3 1.0 HB3 B:CYS4370 3.0 98.2 1.0 H B:CYS4373 3.0 85.7 1.0 CB B:CYS4370 3.1 81.9 1.0 HB2 B:CYS4383 3.1 85.6 1.0 HB2 B:CYS4370 3.1 98.2 1.0 HB3 B:CYS4373 3.3 71.7 1.0 CB B:CYS4383 3.3 71.4 1.0 CB B:CYS4373 3.4 59.9 1.0 HB B:VAL4372 3.5 102.0 1.0 H B:CYS4383 3.6 102.0 1.0 CB B:CYS4381 3.6 77.3 1.0 HB2 B:CYS4381 3.6 92.5 1.0 HA B:CYS4381 3.7 91.8 1.0 N B:CYS4373 3.7 71.5 1.0 HB3 B:CYS4383 4.0 85.6 1.0 CA B:CYS4381 4.1 76.6 1.0 CA B:CYS4373 4.2 83.5 1.0 H B:SER4382 4.2 96.4 1.0 HB2 B:CYS4373 4.2 71.7 1.0 N B:CYS4383 4.2 85.1 1.0 H B:VAL4372 4.3 89.8 1.0 HB3 B:CYS4381 4.4 92.5 1.0 CB B:VAL4372 4.4 85.1 1.0 CA B:CYS4383 4.4 77.7 1.0 O B:HOH4552 4.5 57.1 1.0 H B:MET4375 4.5 70.2 1.0 H B:GLY4374 4.5 76.6 1.0 O B:HOH4531 4.5 63.8 1.0 CA B:CYS4370 4.5 71.8 1.0 N B:SER4382 4.6 80.5 1.0 C B:CYS4381 4.7 87.3 1.0 C B:VAL4372 4.8 63.7 1.0 HA B:CYS4383 4.9 93.0 1.0 HG12 B:VAL4372 4.9 76.2 1.0 C B:CYS4373 4.9 70.6 1.0 HA B:CYS4370 4.9 86.0 1.0 N B:GLY4374 4.9 64.0 1.0 HA B:CYS4373 5.0 100.0 1.0 N B:VAL4372 5.0 75.0 1.0 C B:CYS4370 5.0 76.4 1.0 HB2 B:MET4375 5.0 68.7 1.0 O B:CYS4370 5.0 64.9 1.0 CA B:VAL4372 5.0 60.9 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.