Zinc in PDB 7ult: Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.

The structure of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form., PDB code: 7ult was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.90 / 1.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	166.681, 166.681, 98.55, 90, 90, 120
R / Rfree (%)	16.4 / 18.8

The structure of Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. also contains other interesting chemical elements:

Sodium

(Na)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. (pdb code 7ult). 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 NSP16/10 Heterodimer Apo-Form., PDB code: 7ult:
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 NSP16/10 Heterodimer Apo-Form.


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 NSP16/10 Heterodimer Apo-Form. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4401 b:34.2 occ:1.00 NE2 B:HIS4336 2.1 43.2 1.0 SG B:CYS4327 2.3 35.4 1.0 SG B:CYS4343 2.3 38.0 1.0 SG B:CYS4330 2.3 35.8 1.0 CD2 B:HIS4336 3.0 44.5 1.0 CE1 B:HIS4336 3.1 44.1 1.0 CB B:CYS4327 3.2 34.7 1.0 CB B:CYS4343 3.3 41.6 1.0 CB B:CYS4330 3.4 35.0 1.0 N B:CYS4330 3.6 34.8 1.0 CA B:CYS4330 3.9 34.5 1.0 ND1 B:HIS4336 4.2 44.3 1.0 CG B:HIS4336 4.2 44.0 1.0 O B:HOH4607 4.3 32.2 0.5 O B:HOH4570 4.3 45.2 1.0 CA B:CYS4343 4.4 43.3 1.0 CB B:TYR4329 4.5 37.8 1.0 C B:TYR4329 4.5 36.5 1.0 CA B:CYS4327 4.6 33.2 1.0 CB B:LYS4346 4.9 33.7 1.0 CA B:TYR4329 4.9 36.9 1.0 N B:LYS4346 5.0 31.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


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 NSP16/10 Heterodimer Apo-Form. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn4402 b:45.1 occ:1.00 SG B:CYS4381 2.3 40.6 1.0 SG B:CYS4370 2.3 48.9 1.0 SG B:CYS4373 2.3 47.9 1.0 SG B:CYS4383 2.3 53.2 1.0 CB B:CYS4370 3.1 47.9 1.0 CB B:CYS4373 3.3 49.4 1.0 CB B:CYS4383 3.3 57.3 1.0 CB B:CYS4381 3.4 45.2 1.0 N B:CYS4373 3.6 50.9 1.0 O B:HOH4550 3.9 42.4 1.0 CA B:CYS4373 4.0 48.1 1.0 CA B:CYS4381 4.1 45.0 1.0 N B:CYS4383 4.1 55.0 1.0 CA B:CYS4383 4.3 57.2 1.0 CB B:VAL4372 4.4 59.0 1.0 O B:HOH4597 4.5 61.4 1.0 CA B:CYS4370 4.6 46.2 1.0 N B:SER4382 4.6 49.7 1.0 C B:VAL4372 4.6 53.8 1.0 C B:CYS4381 4.6 46.7 1.0 C B:CYS4373 4.8 46.0 1.0 CA B:VAL4372 4.9 55.7 1.0 N B:GLY4374 4.9 43.6 1.0 N B:VAL4372 4.9 54.5 1.0 CG1 B:VAL4372 5.0 60.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


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 NSP16/10 Heterodimer Apo-Form. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4401 b:30.4 occ:1.00 NE2 D:HIS4336 2.1 34.8 1.0 SG D:CYS4327 2.3 32.5 1.0 SG D:CYS4330 2.3 32.9 1.0 SG D:CYS4343 2.3 32.7 1.0 CD2 D:HIS4336 3.1 36.8 1.0 CE1 D:HIS4336 3.1 35.9 1.0 CB D:CYS4327 3.2 31.4 1.0 CB D:CYS4343 3.3 35.0 1.0 CB D:CYS4330 3.4 32.8 1.0 N D:CYS4330 3.6 33.8 1.0 CA D:CYS4330 3.9 32.6 1.0 CG D:HIS4336 4.2 38.2 1.0 ND1 D:HIS4336 4.2 36.0 1.0 O D:HOH4529 4.3 45.1 1.0 CA D:CYS4343 4.3 36.0 1.0 CB D:TYR4329 4.5 36.8 1.0 C D:TYR4329 4.6 34.1 1.0 CA D:CYS4327 4.6 30.3 1.0 CB D:LYS4346 4.8 34.7 1.0 CA D:TYR4329 4.9 35.4 1.0 N D:LYS4346 5.0 30.0 1.0 C D:CYS4327 5.0 30.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form.


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 NSP16/10 Heterodimer Apo-Form. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn4402 b:46.1 occ:1.00 SG D:CYS4381 2.3 45.6 1.0 SG D:CYS4370 2.3 51.7 1.0 SG D:CYS4373 2.3 46.7 1.0 SG D:CYS4383 2.3 57.4 1.0 CB D:CYS4370 3.1 49.8 1.0 CB D:CYS4373 3.4 48.4 1.0 CB D:CYS4383 3.4 64.8 1.0 CB D:CYS4381 3.5 47.7 1.0 N D:CYS4373 3.7 49.5 1.0 O D:HOH4541 3.9 56.7 1.0 CA D:CYS4381 4.1 46.1 1.0 CA D:CYS4373 4.1 47.1 1.0 N D:CYS4383 4.1 62.5 1.0 CA D:CYS4383 4.3 66.9 1.0 CB D:VAL4372 4.5 56.9 1.0 N D:SER4382 4.6 52.0 1.0 CA D:CYS4370 4.6 48.3 1.0 C D:CYS4381 4.6 48.6 1.0 C D:VAL4372 4.7 52.6 1.0 C D:CYS4373 4.9 43.6 1.0 CA D:VAL4372 5.0 55.0 1.0

G.Minasov, L.Shuvalova, J.S.Brunzelle, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Sars-Cov-2 NSP16/10 Heterodimer Apo-Form. To Be Published.