Zinc in PDB 7thm: Sars-Cov-2 NSP12/7/8 Complex with A Native N-Terminus NSP9

All present enzymatic activity of Sars-Cov-2 NSP12/7/8 Complex with A Native N-Terminus NSP9:
2.7.7.48;

The structure of Sars-Cov-2 NSP12/7/8 Complex with A Native N-Terminus NSP9 also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Zinc atom in the Sars-Cov-2 NSP12/7/8 Complex with A Native N-Terminus NSP9 (pdb code 7thm). 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 NSP12/7/8 Complex with A Native N-Terminus NSP9, PDB code: 7thm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sars-Cov-2 NSP12/7/8 Complex with A Native N-Terminus NSP9


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 NSP12/7/8 Complex with A Native N-Terminus NSP9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:62.4 occ:1.00 ND1 A:HIS295 2.1 46.1 1.0 SG A:CYS301 2.3 48.6 1.0 SG A:CYS310 2.3 44.9 1.0 SG A:CYS306 2.3 47.3 1.0 CE1 A:HIS295 2.8 46.1 1.0 HE1 A:HIS295 2.8 46.1 1.0 HA A:CYS301 2.9 48.6 1.0 CB A:CYS301 3.2 48.6 1.0 HB3 A:CYS301 3.2 48.6 1.0 CG A:HIS295 3.3 46.1 1.0 HB2 A:HIS295 3.3 46.1 1.0 O A:CYS306 3.4 47.3 1.0 CA A:CYS301 3.5 48.6 1.0 HB2 A:CYS310 3.5 44.9 1.0 CB A:CYS310 3.6 44.9 1.0 H A:HIS295 3.6 46.1 1.0 CB A:CYS306 3.7 47.3 1.0 CB A:HIS295 3.8 46.1 1.0 C A:CYS306 3.8 47.3 1.0 HB3 A:CYS306 3.9 47.3 1.0 NE2 A:HIS295 4.0 46.1 1.0 HB3 A:CYS310 4.1 44.9 1.0 HB2 A:CYS301 4.1 48.6 1.0 HA A:ILE307 4.2 45.6 1.0 N A:CYS301 4.2 48.6 1.0 CD2 A:HIS295 4.2 46.1 1.0 CA A:CYS306 4.3 47.3 1.0 N A:HIS295 4.3 46.1 1.0 H A:CYS310 4.4 44.9 1.0 HA A:CYS298 4.4 46.5 1.0 H A:LEU302 4.4 48.8 1.0 H A:CYS301 4.4 48.6 1.0 HA A:CYS306 4.4 47.3 1.0 HB2 A:CYS306 4.5 47.3 1.0 N A:ILE307 4.5 45.6 1.0 HB3 A:HIS295 4.5 46.1 1.0 O A:THR293 4.6 48.3 1.0 CA A:HIS295 4.7 46.1 1.0 HA A:TYR294 4.7 46.2 1.0 C A:CYS301 4.8 48.6 1.0 CA A:ILE307 4.8 45.6 1.0 CA A:CYS310 4.8 44.9 1.0 C A:ASN300 4.9 46.9 1.0 N A:CYS310 4.9 44.9 1.0 ND1 A:HIS309 4.9 44.7 1.0 N A:LEU302 4.9 48.8 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 NSP12/7/8 Complex with A Native N-Terminus NSP9


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 NSP12/7/8 Complex with A Native N-Terminus NSP9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:76.1 occ:1.00 ND1 A:HIS642 2.1 55.2 1.0 SG A:CYS487 2.3 57.9 1.0 SG A:CYS646 2.3 58.0 1.0 SG A:CYS645 2.3 61.3 1.0 HB3 A:HIS642 2.8 55.2 1.0 CE1 A:HIS642 3.0 55.2 1.0 CG A:HIS642 3.0 55.2 1.0 HB2 A:CYS646 3.0 58.0 1.0 HE1 A:HIS642 3.2 55.2 1.0 HB2 A:CYS487 3.2 57.9 1.0 CB A:CYS646 3.2 58.0 1.0 CB A:HIS642 3.4 55.2 1.0 HE1 A:PHE571 3.4 53.4 1.0 CB A:CYS487 3.4 57.9 1.0 H A:CYS487 3.5 57.9 1.0 CB A:CYS645 3.8 61.3 1.0 HZ3 A:LYS532 3.8 54.5 1.0 HB2 A:CYS645 3.8 61.3 1.0 HB3 A:CYS646 4.0 58.0 1.0 NE2 A:HIS642 4.0 55.2 1.0 N A:CYS646 4.0 58.0 1.0 HB2 A:HIS642 4.0 55.2 1.0 CD2 A:HIS642 4.0 55.2 1.0 HZ1 A:LYS532 4.1 54.5 1.0 C A:CYS645 4.1 61.3 1.0 HB3 A:CYS487 4.1 57.9 1.0 N A:CYS487 4.1 57.9 1.0 CE1 A:PHE571 4.2 53.4 1.0 CA A:CYS646 4.2 58.0 1.0 H A:CYS646 4.2 58.0 1.0 HA A:HIS642 4.2 55.2 1.0 HD1 A:PHE571 4.2 53.4 1.0 HE2 A:LYS532 4.3 54.5 1.0 NZ A:LYS532 4.3 54.5 1.0 CA A:CYS487 4.4 57.9 1.0 CA A:HIS642 4.4 55.2 1.0 O A:CYS645 4.4 61.3 1.0 HB3 A:CYS645 4.5 61.3 1.0 HA A:CYS646 4.5 58.0 1.0 CA A:CYS645 4.6 61.3 1.0 CD1 A:PHE571 4.6 53.4 1.0 HA A:CYS487 4.7 57.9 1.0 HZ A:PHE528 4.8 58.1 1.0 HD2 A:HIS642 4.8 55.2 1.0 CE A:LYS532 4.8 54.5 1.0 HG3 A:ARG651 4.9 52.0 1.0 O A:HIS642 5.0 55.2 1.0 H A:CYS645 5.0 61.3 1.0

V.Tagliabracci, G.Park, A.Osinski, G.Hernandez, J.Eitson, A.Majumdar, M.Tonelli, K.Henzler-Wildman, K.Pawlowski, Z.Chen, Y.Li, J.Schoggins. The Mechanism of Rna Capping By Sars-Cov-2. Res Sq 2022.
ISSN: ESSN 2693-5015
PubMed: 35194601
DOI: 10.21203/RS.3.RS-1336910/V1