Structure of PDB 6agg Chain Z Binding Site BS04

Receptor Information

>6agg Chain Z (length=420) Species: 224325 (Archaeoglobus fulgidus DSM 4304)

MRVWVGIDDTDSSRGMCTTYLAVLAMERVERELGKVIGFPRLIRLNPTIP
YKTRGNGAVSFLVEVDDVGELVDVVNEVIIEHAMLDDEKTNPGAVFVDEE
LAVKLKPFADKAIKDVLQIDEALFVIGKYFIPHLRHKKGRGLIGALAAVG
AELEDFTLELIAYRYPERFGTEREYDEESFFDMDYELYPQTFDNVDWCND
VVVCIPNTPCPVLYGIRGESVEALYKAMESVKTEPVDRRMIFVTNHATDM
HLIGEEEVHRLENYRSYRLRGRVTLEPYDIEGGHVFFEIDTKFGSVKCAA
FEPTKQFRNVIRLLRKGDVVEVYGSMKKDTINLEKIQIVELAEIWVEKNP
ICPSCGRRMESAGRGQGFRCKKCRTKADEKLREKVERELQPGFYEVPPSA
RRHLSKPLIRMNVEGRHIFR

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 6agg Chain Z Residue 508

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6agg Structure of tRNA-Modifying Enzyme TiaS and Motions of Its Substrate Binding Zinc Ribbon.
• Resolution: 2.706 Å
• Binding residue (original residue number in PDB): D8 T18 G57 A58
• Binding residue (residue number reindexed from 1): D8 T18 G57 A58
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 6.3.4.22: tRNA(Ile)(2)-agmatinylcytidine synthase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0016879 ligase activity, forming carbon-nitrogen bonds

Biological Process

• GO:0002101 tRNA wobble cytosine modification
• GO:0008033 tRNA processing

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6agg, PDBe:6agg, PDBj:6agg
• PDBsum: 6agg
• PubMed: 30121296
• UniProt: O28025|TIAS_ARCFU tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS (Gene Name=tiaS)