Zinc in PDB 6xqb: Sars-Cov-2 Rdrp/Rna Complex

All present enzymatic activity of Sars-Cov-2 Rdrp/Rna Complex:
2.7.7.48; 3.4.19.12;

The structure of Sars-Cov-2 Rdrp/Rna Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Sars-Cov-2 Rdrp/Rna Complex (pdb code 6xqb). 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 Rdrp/Rna Complex, PDB code: 6xqb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sars-Cov-2 Rdrp/Rna Complex


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 Rdrp/Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:0.4 occ:1.00 HA A:CYS301 1.8 0.3 1.0 HG A:CYS310 1.8 0.4 1.0 HD2 A:HIS295 1.9 0.7 1.0 HB2 A:HIS295 2.0 0.7 1.0 CD2 A:HIS295 2.4 0.7 1.0 SG A:CYS306 2.4 0.2 1.0 SG A:CYS301 2.4 0.3 1.0 CA A:CYS301 2.5 0.3 1.0 CG A:HIS295 2.6 0.7 1.0 CB A:HIS295 2.7 0.7 1.0 CB A:CYS301 2.7 0.3 1.0 HB3 A:CYS301 2.8 0.3 1.0 SG A:CYS310 3.0 0.4 1.0 H A:LEU302 3.0 0.1 1.0 HB3 A:HIS295 3.3 0.7 1.0 N A:CYS301 3.5 0.3 1.0 HB3 A:CYS306 3.5 0.2 1.0 NE2 A:HIS295 3.6 0.7 1.0 N A:LEU302 3.6 0.1 1.0 HB2 A:CYS310 3.6 0.4 1.0 C A:CYS301 3.6 0.3 1.0 CB A:CYS306 3.6 0.2 1.0 HB2 A:CYS301 3.6 0.3 1.0 HG23 A:THR293 3.7 0.6 1.0 O A:CYS306 3.7 0.2 1.0 HD23 A:LEU302 3.8 0.1 1.0 CA A:HIS295 3.8 0.7 1.0 H A:CYS301 3.8 0.3 1.0 N A:HIS295 3.9 0.7 1.0 ND1 A:HIS295 3.9 0.7 1.0 HD22 A:LEU302 3.9 0.1 1.0 CB A:CYS310 3.9 0.4 1.0 H A:HIS295 3.9 0.7 1.0 C A:ASN300 4.1 0.8 1.0 O A:ASN300 4.1 0.8 1.0 C A:CYS306 4.2 0.2 1.0 HD1 A:HIS309 4.2 0.7 1.0 HA A:CYS298 4.3 0.5 1.0 CE1 A:HIS295 4.3 0.7 1.0 CD2 A:LEU302 4.3 0.1 1.0 HB2 A:CYS306 4.3 0.2 1.0 HB3 A:CYS310 4.3 0.4 1.0 C A:TYR294 4.4 0.9 1.0 HG21 A:THR293 4.5 0.6 1.0 O A:HIS295 4.5 0.7 1.0 CG2 A:THR293 4.5 0.6 1.0 HD1 A:HIS295 4.5 0.7 1.0 CA A:CYS306 4.5 0.2 1.0 H A:CYS310 4.5 0.4 1.0 HA A:HIS295 4.6 0.7 1.0 C A:HIS295 4.6 0.7 1.0 O A:TYR294 4.7 0.9 1.0 HD21 A:LEU302 4.8 0.1 1.0 O A:CYS301 4.8 0.3 1.0 HA A:ILE307 4.8 0.9 1.0 HA A:CYS306 4.8 0.2 1.0 HB3 A:HIS309 4.9 0.7 1.0 HB2 A:LEU302 4.9 0.1 1.0 HG1 A:THR293 4.9 0.6 1.0 HG22 A:THR293 4.9 0.6 1.0 HB2 A:ASN300 5.0 0.8 1.0 CA A:LEU302 5.0 0.1 1.0 HA A:TYR294 5.0 0.9 1.0 N A:ILE307 5.0 0.9 1.0 ND1 A:HIS309 5.0 0.7 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 Rdrp/Rna Complex


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 Rdrp/Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:0.3 occ:1.00 HD1 A:HIS642 1.6 0.7 1.0 HB3 A:HIS642 1.7 0.7 1.0 ND1 A:HIS642 2.2 0.7 1.0 SG A:CYS487 2.3 0.5 1.0 SG A:CYS645 2.4 0.8 1.0 CB A:HIS642 2.4 0.7 1.0 SG A:CYS646 2.4 0.5 1.0 CG A:HIS642 2.6 0.7 1.0 H A:CYS487 3.0 0.5 1.0 HA A:HIS642 3.0 0.7 1.0 HB2 A:CYS646 3.1 0.5 1.0 HB2 A:HIS642 3.2 0.7 1.0 CA A:HIS642 3.2 0.7 1.0 CB A:CYS646 3.3 0.5 1.0 HB2 A:CYS645 3.3 0.8 1.0 O A:HIS642 3.4 0.7 1.0 CB A:CYS645 3.4 0.8 1.0 C A:CYS645 3.4 0.8 1.0 CB A:CYS487 3.4 0.5 1.0 N A:CYS646 3.4 0.5 1.0 HB2 A:CYS487 3.5 0.5 1.0 CE1 A:HIS642 3.5 0.7 1.0 H A:CYS646 3.6 0.5 1.0 N A:CYS487 3.7 0.5 1.0 O A:CYS645 3.7 0.8 1.0 H A:CYS645 3.7 0.8 1.0 C A:HIS642 3.7 0.7 1.0 CA A:CYS645 3.8 0.8 1.0 CD2 A:HIS642 3.9 0.7 1.0 CA A:CYS646 3.9 0.5 1.0 HE1 A:HIS642 3.9 0.7 1.0 CA A:CYS487 4.0 0.5 1.0 HB3 A:CYS646 4.1 0.5 1.0 HB3 A:CYS645 4.2 0.8 1.0 HA2 A:GLY486 4.2 0.6 1.0 HA A:CYS646 4.2 0.5 1.0 N A:CYS645 4.3 0.8 1.0 HB3 A:CYS487 4.3 0.5 1.0 NE2 A:HIS642 4.3 0.7 1.0 HA A:CYS487 4.3 0.5 1.0 N A:HIS642 4.5 0.7 1.0 HE1 A:PHE571 4.6 0.2 1.0 HD2 A:HIS642 4.6 0.7 1.0 C A:GLY486 4.7 0.6 1.0 HZ A:PHE528 4.7 0.2 1.0 HA A:CYS645 4.7 0.8 1.0 H A:HIS642 4.8 0.7 1.0 CE1 A:PHE571 4.9 0.2 1.0 H A:THR644 4.9 0.5 1.0 CA A:GLY486 4.9 0.6 1.0

B.Liu, W.Shi, Y.Yang. Structure of Sars-Cov-2 Rdrp/Rna Complex at 3.4 Angstroms Resolution To Be Published.