Zinc in PDB 8sq9: Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate

All present enzymatic activity of Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate:
2.7.7.48;

The structure of Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate (pdb code 8sq9). 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 NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate, PDB code: 8sq9:
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 NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate


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 NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:128.6 occ:1.00 ND1 A:HIS295 2.2 77.2 1.0 SG A:CYS310 2.3 68.5 1.0 SG A:CYS301 2.3 78.4 1.0 SG A:CYS306 2.3 82.2 1.0 HB2 A:HIS295 2.8 72.8 1.0 HA A:CYS301 2.9 70.9 1.0 O A:CYS306 3.1 74.6 1.0 CE1 A:HIS295 3.2 72.5 1.0 CG A:HIS295 3.2 71.2 1.0 CB A:CYS301 3.3 69.1 1.0 HE1 A:HIS295 3.4 73.4 1.0 HB3 A:CYS301 3.4 71.0 1.0 CB A:HIS295 3.5 64.0 1.0 CA A:CYS301 3.6 66.3 1.0 HB2 A:CYS310 3.6 66.0 1.0 CB A:CYS310 3.7 63.0 1.0 H A:HIS295 3.7 73.3 1.0 CB A:CYS306 3.8 64.1 1.0 C A:CYS306 3.8 64.7 1.0 HB3 A:CYS306 4.0 67.8 1.0 H A:LEU302 4.1 72.9 1.0 HB3 A:CYS310 4.1 66.6 1.0 HB3 A:HIS295 4.1 72.9 1.0 HB2 A:CYS301 4.2 71.1 1.0 HD1 A:HIS309 4.2 63.5 1.0 NE2 A:HIS295 4.3 68.6 1.0 CA A:CYS306 4.3 65.5 1.0 N A:HIS295 4.3 71.3 1.0 CD2 A:HIS295 4.3 69.8 1.0 HA A:CYS306 4.4 68.2 1.0 H A:CYS310 4.4 66.5 1.0 HA A:ILE307 4.4 65.3 1.0 N A:CYS301 4.4 68.5 1.0 CA A:HIS295 4.5 65.5 1.0 HB2 A:CYS306 4.5 67.6 1.0 H A:CYS301 4.7 70.7 1.0 N A:LEU302 4.7 76.3 1.0 N A:ILE307 4.7 61.1 1.0 HA A:CYS298 4.7 67.1 1.0 C A:CYS301 4.7 73.2 1.0 HG23 A:THR293 4.7 66.2 1.0 HG A:LEU302 4.8 72.5 1.0 CA A:CYS310 4.9 62.9 1.0 N A:CYS310 4.9 64.7 1.0 O A:THR293 4.9 66.9 1.0 O A:HIS295 5.0 76.2 1.0

Zinc binding site 2 out of 2 in the Sars-Cov-2 Replication-Transcription Complex Bound to NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate


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 NSP9 and Umpcpp, As A Pre-Catalytic Nmpylation Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:122.0 occ:1.00 HD1 A:HIS642 1.5 69.0 1.0 SG A:CYS487 1.7 61.7 1.0 SG A:CYS646 2.2 79.2 1.0 SG A:CYS645 2.3 69.5 1.0 ND1 A:HIS642 2.3 68.6 1.0 HB3 A:HIS642 2.9 68.5 1.0 HE1 A:PHE571 3.2 71.3 1.0 CE1 A:HIS642 3.2 66.9 1.0 CB A:CYS487 3.3 72.0 1.0 CG A:HIS642 3.3 64.5 1.0 HE1 A:HIS642 3.4 69.1 1.0 HB2 A:CYS487 3.4 69.5 1.0 H A:CYS487 3.4 68.1 1.0 HB2 A:CYS645 3.5 72.7 1.0 CB A:HIS642 3.6 62.2 1.0 CB A:CYS645 3.6 70.2 1.0 CE1 A:PHE571 3.6 74.0 1.0 CB A:CYS646 3.6 65.0 1.0 HB2 A:CYS646 3.7 70.6 1.0 N A:CYS487 3.8 67.5 1.0 HZ A:PHE571 3.8 71.1 1.0 HB3 A:CYS487 3.9 67.8 1.0 HZ1 A:LYS532 3.9 68.0 1.0 CZ A:PHE571 4.0 70.2 1.0 N A:CYS646 4.1 72.5 1.0 C A:CYS645 4.1 75.3 1.0 CA A:CYS487 4.1 72.3 1.0 HA A:HIS642 4.1 68.6 1.0 H A:CYS646 4.3 71.3 1.0 HB3 A:CYS645 4.3 72.8 1.0 HB2 A:HIS642 4.3 68.5 1.0 HE2 A:LYS532 4.3 68.0 1.0 HZ3 A:LYS532 4.3 67.5 1.0 HA2 A:GLY486 4.3 67.7 1.0 HB3 A:CYS646 4.3 70.7 1.0 NE2 A:HIS642 4.4 64.2 1.0 HA A:CYS487 4.4 68.4 1.0 CA A:CYS645 4.4 70.4 1.0 O A:CYS645 4.4 76.7 1.0 CD2 A:HIS642 4.4 64.8 1.0 CA A:CYS646 4.4 69.9 1.0 CD1 A:PHE571 4.4 77.9 1.0 CA A:HIS642 4.4 61.5 1.0 NZ A:LYS532 4.5 70.7 1.0 HD1 A:PHE571 4.6 72.2 1.0 H A:CYS645 4.6 73.4 1.0 C A:GLY486 4.6 67.6 1.0 HA A:CYS646 4.7 71.7 1.0 HZ A:PHE528 4.7 66.0 1.0 O A:HIS642 4.9 74.8 1.0 CE A:LYS532 4.9 69.5 1.0 CA A:GLY486 4.9 69.7 1.0 CE2 A:PHE571 5.0 67.8 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