Zinc in PDB 8vuo: Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna

The structure of Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna, PDB code: 8vuo was solved by A.Misra, R.Rahisuddin, Y.K.Gupta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.70 / 2.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	111.747, 58.893, 117.021, 90, 95.48, 90
R / Rfree (%)	18 / 21.9

The structure of Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna (pdb code 8vuo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna, PDB code: 8vuo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:33.6 occ:1.00 NE2 B:HIS83 2.1 36.6 1.0 SG B:CYS74 2.2 31.5 1.0 SG B:CYS77 2.3 35.3 1.0 SG B:CYS90 2.3 33.1 1.0 CD2 B:HIS83 3.0 29.6 1.0 CB B:CYS74 3.1 30.3 1.0 CE1 B:HIS83 3.2 40.5 1.0 CB B:CYS90 3.3 31.4 1.0 CB B:CYS77 3.4 29.3 1.0 N B:CYS77 3.6 30.6 1.0 CA B:CYS77 4.0 43.2 1.0 O B:HOH359 4.0 51.8 1.0 CG B:HIS83 4.2 40.3 1.0 ND1 B:HIS83 4.3 34.3 1.0 CA B:CYS74 4.6 34.4 1.0 CB B:LYS93 4.6 26.4 1.0 CA B:CYS90 4.6 41.3 1.0 C B:TYR76 4.6 33.8 1.0 CB B:TYR76 4.7 30.1 1.0 N B:LYS93 4.7 27.2 1.0 C B:CYS74 5.0 29.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:63.0 occ:1.00 SG B:CYS117 2.3 59.6 1.0 SG B:CYS128 2.4 57.4 1.0 SG B:CYS120 2.5 55.5 1.0 SG B:CYS130 2.5 87.6 1.0 CB B:CYS117 3.1 48.4 1.0 CB B:CYS130 3.3 78.0 1.0 CB B:CYS120 3.5 63.8 1.0 CB B:CYS128 3.6 56.7 1.0 N B:CYS120 3.9 60.9 1.0 O B:HOH341 4.2 58.4 1.0 N B:CYS130 4.2 80.1 1.0 CA B:CYS128 4.3 55.0 1.0 CA B:CYS120 4.3 62.1 1.0 CA B:CYS130 4.4 77.8 1.0 CA B:CYS117 4.5 49.6 1.0 CB B:VAL119 4.7 60.8 1.0 N B:SER129 4.7 76.6 1.0 C B:CYS128 4.8 64.4 1.0 C B:VAL119 5.0 66.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:34.1 occ:1.00 NE2 D:HIS83 2.2 34.9 1.0 SG D:CYS74 2.2 35.5 1.0 SG D:CYS77 2.3 35.3 1.0 SG D:CYS90 2.4 32.7 1.0 CD2 D:HIS83 3.0 30.5 1.0 CB D:CYS74 3.1 37.5 1.0 CE1 D:HIS83 3.3 36.1 1.0 CB D:CYS90 3.3 32.4 1.0 CB D:CYS77 3.4 34.4 1.0 N D:CYS77 3.6 34.3 1.0 CA D:CYS77 4.0 41.9 1.0 O D:HOH362 4.1 46.5 1.0 CG D:HIS83 4.2 36.1 1.0 ND1 D:HIS83 4.3 32.0 1.0 CA D:CYS74 4.6 35.5 1.0 CA D:CYS90 4.6 46.9 1.0 CB D:LYS93 4.6 29.2 1.0 C D:TYR76 4.7 35.9 1.0 CB D:TYR76 4.7 29.3 1.0 N D:LYS93 4.8 29.2 1.0 C D:CYS74 5.0 32.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:59.5 occ:1.00 SG D:CYS128 2.4 61.3 1.0 SG D:CYS117 2.4 56.2 1.0 SG D:CYS120 2.4 51.0 1.0 SG D:CYS130 2.5 87.0 1.0 CB D:CYS117 3.2 45.4 1.0 CB D:CYS120 3.4 50.0 1.0 CB D:CYS130 3.4 73.6 1.0 CB D:CYS128 3.7 51.6 1.0 N D:CYS120 3.8 57.3 1.0 CA D:CYS120 4.2 51.9 1.0 N D:CYS130 4.2 68.5 1.0 CA D:CYS128 4.3 61.2 1.0 CA D:CYS130 4.4 78.7 1.0 CA D:CYS117 4.6 48.1 1.0 CB D:VAL119 4.7 62.6 1.0 N D:SER129 4.8 64.4 1.0 C D:CYS128 4.9 60.0 1.0 C D:VAL119 4.9 51.4 1.0 NZ D:LYS124 5.0 79.5 1.0 C D:CYS120 5.0 55.7 1.0

A.Misra, R.Rahisuddin, Y.K.Gupta. Crystal Structure of Sars-Cov-2 NSP16/NSP10 in Complex with Cap-1 Rna To Be Published.