Structure of PDB 5d4b Chain B Binding Site BS04

Receptor Information

>5d4b Chain B (length=349) Species: 10090 (Mus musculus)

KISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVL
KSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKS
FKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYED
LVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLI
TSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQALDHFQKC
FLILKLDHGRVHEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLR
RYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA

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: 5d4b Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d4b Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination.
• Resolution: 2.66 Å
• Binding residue (original residue number in PDB): D343 D345
• Binding residue (residue number reindexed from 1): D195 D197
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D343 D345 D434
• Catalytic site (residue number reindexed from 1): D195 D197 D273
• Enzyme Commision number: 2.7.7.31: DNA nucleotidylexotransferase.
  3.1.11.-

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0034061 DNA polymerase activity

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:5d4b, PDBe:5d4b, PDBj:5d4b
• PDBsum: 5d4b
• PubMed: 27499438
• UniProt: P09838|TDT_MOUSE DNA nucleotidylexotransferase (Gene Name=Dntt)