Structure of PDB 7jyy Chain B Binding Site BS02

Receptor Information

>7jyy Chain B (length=129) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

STVLSFCAFAVDAAKAYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPE
ANMDQESFGGASCCLYCRCHIDHPNPKGFCDLKGKYVQIPTTCANDPVGF
TLKNTVCTVCGMWKGYGCSCDQLREPMLQ

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 7jyy Chain B Residue 4402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7jyy Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16.
• Resolution: 2.05 Å
• Binding residue (original residue number in PDB): C4370 C4373 C4381 C4383
• Binding residue (residue number reindexed from 1): C107 C110 C118 C120
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0008270 zinc ion binding

Biological Process

• GO:0019079 viral genome replication

External links

• PDB: RCSB:7jyy, PDBe:7jyy, PDBj:7jyy
• PDBsum: 7jyy
• PubMed: 34131072
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)