Zinc in PDB 8sqj: Sars-Cov-2 Replication-Transcription Complex Bound to Rna-NSP9, As A Noncatalytic Rna-NSP9 Binding Mode

All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to Rna-NSP9, As A Noncatalytic Rna-NSP9 Binding Mode:
2.7.7.48;

The structure of Sars-Cov-2 Replication-Transcription Complex Bound to Rna-NSP9, As A Noncatalytic Rna-NSP9 Binding Mode also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Sars-Cov-2 Replication-Transcription Complex Bound to Rna-NSP9, As A Noncatalytic Rna-NSP9 Binding Mode (pdb code 8sqj). 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 Replication-Transcription Complex Bound to Rna-NSP9, As A Noncatalytic Rna-NSP9 Binding Mode, PDB code: 8sqj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Sars-Cov-2 Replication-Transcription Complex Bound to Rna-NSP9, As A Noncatalytic Rna-NSP9 Binding Mode


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 Replication-Transcription Complex Bound to Rna-NSP9, As A Noncatalytic Rna-NSP9 Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1003 b:93.0 occ:1.00 O A:HOH1159 1.8 37.4 1.0 ND1 A:HIS295 2.3 29.2 1.0 SG A:CYS301 2.3 31.1 1.0 SG A:CYS310 2.3 30.2 1.0 SG A:CYS306 2.3 41.2 1.0 O A:CYS306 3.0 39.4 1.0 HB2 A:HIS295 3.1 19.6 1.0 CE1 A:HIS295 3.2 13.2 1.0 HE1 A:HIS295 3.3 19.0 1.0 HA A:CYS301 3.3 26.2 1.0 CG A:HIS295 3.3 20.6 1.0 CB A:CYS301 3.5 24.9 1.0 HB3 A:CYS301 3.5 27.5 1.0 H A:HIS295 3.6 21.0 1.0 CB A:HIS295 3.7 16.9 1.0 CB A:CYS310 3.8 23.3 1.0 HB2 A:CYS310 3.8 25.4 1.0 CB A:CYS306 3.9 20.5 1.0 CA A:CYS301 3.9 17.8 1.0 C A:CYS306 3.9 27.8 1.0 HB3 A:CYS306 4.1 29.4 1.0 HB3 A:CYS310 4.2 23.7 1.0 N A:HIS295 4.2 22.1 1.0 HD1 A:HIS309 4.3 24.3 1.0 HB2 A:CYS301 4.3 26.4 1.0 NE2 A:HIS295 4.3 17.6 1.0 H A:CYS310 4.4 24.3 1.0 H A:LEU302 4.4 31.0 1.0 CA A:CYS306 4.4 22.4 1.0 HB3 A:HIS295 4.4 20.6 1.0 CD2 A:HIS295 4.4 21.7 1.0 HA A:CYS306 4.5 29.8 1.0 HA A:ILE307 4.6 25.6 1.0 HB2 A:CYS306 4.6 29.7 1.0 CA A:HIS295 4.6 12.3 1.0 HG23 A:THR293 4.7 27.3 1.0 HA A:TYR294 4.7 18.9 1.0 O A:THR293 4.7 31.8 1.0 N A:CYS301 4.7 28.4 1.0 HG A:LEU302 4.8 30.4 1.0 HA A:CYS298 4.9 23.4 1.0 HB3 A:HIS309 4.9 24.5 1.0 N A:CYS310 4.9 19.9 1.0 N A:ILE307 4.9 29.8 1.0 CA A:CYS310 5.0 12.1 1.0 N A:LEU302 5.0 32.9 1.0 H A:CYS301 5.0 27.0 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 Replication-Transcription Complex Bound to Rna-NSP9, As A Noncatalytic Rna-NSP9 Binding Mode


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 Replication-Transcription Complex Bound to Rna-NSP9, As A Noncatalytic Rna-NSP9 Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1004 b:80.7 occ:1.00 ND1 A:HIS642 2.2 30.2 1.0 SG A:CYS487 2.3 44.2 1.0 SG A:CYS645 2.3 38.3 1.0 SG A:CYS646 2.3 49.0 1.0 HB3 A:HIS642 2.7 29.9 1.0 CG A:HIS642 3.1 23.8 1.0 CE1 A:HIS642 3.2 29.2 1.0 HE1 A:HIS642 3.4 30.6 1.0 CB A:HIS642 3.4 24.7 1.0 HE1 A:PHE571 3.5 25.7 1.0 CB A:CYS487 3.8 38.4 1.0 H A:CYS487 3.8 36.2 1.0 CB A:CYS646 3.8 32.9 1.0 CB A:CYS645 3.8 41.0 1.0 HB2 A:CYS646 3.9 37.1 1.0 HB2 A:CYS487 3.9 37.7 1.0 HB2 A:CYS645 3.9 41.1 1.0 N A:CYS487 4.1 31.6 1.0 CE1 A:PHE571 4.1 24.0 1.0 HA A:HIS642 4.1 31.4 1.0 HB2 A:HIS642 4.1 29.7 1.0 HA2 A:GLY486 4.2 31.7 1.0 HZ3 A:LYS532 4.2 30.9 1.0 HD1 A:PHE571 4.3 26.3 1.0 NE2 A:HIS642 4.3 23.7 1.0 CD2 A:HIS642 4.3 22.0 1.0 N A:CYS646 4.3 38.8 1.0 C A:CYS645 4.3 41.7 1.0 CA A:HIS642 4.4 32.0 1.0 CA A:CYS487 4.4 36.3 1.0 HB3 A:CYS487 4.5 37.0 1.0 H A:CYS646 4.5 38.3 1.0 CD1 A:PHE571 4.5 23.8 1.0 HB3 A:CYS646 4.5 36.9 1.0 HB3 A:CYS645 4.5 41.3 1.0 HE2 A:LYS532 4.5 29.5 1.0 HA A:CYS487 4.6 36.5 1.0 C A:GLY486 4.6 30.5 1.0 CA A:CYS646 4.6 31.4 1.0 CA A:CYS645 4.7 41.4 1.0 O A:CYS645 4.7 45.1 1.0 H A:CYS645 4.7 42.0 1.0 CA A:GLY486 4.9 25.7 1.0 NZ A:LYS532 4.9 40.1 1.0 HZ2 A:LYS532 4.9 30.8 1.0 CZ A:PHE571 4.9 18.3 1.0 O A:HIS642 4.9 38.2 1.0 HA A:CYS646 4.9 37.2 1.0 HZ A:PHE528 5.0 28.3 1.0

G.I.Small, O.Fedorova, P.D.B.Olinares, J.Chandanani, A.Banerjee, Y.J.Choi, H.Molina, B.T.Chait, S.A.Darst, E.A.Campbell. Structural and Functional Insights Into the Enzymatic Plasticity of the Sars-Cov-2 Niran Domain. Mol.Cell V. 83 3921 2023.
ISSN: ISSN 1097-2765
PubMed: 37890482
DOI: 10.1016/J.MOLCEL.2023.10.001