Structure of PDB 8d3r Chain A Binding Site BS04

Receptor Information
>8d3r Chain A (length=958) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRHNPLDIQMLSRGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQPAV
PLPDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPA
WAWAEGWTRYGPEGEAVPVAIPEERALVFDVEVCLAEGTCPTLAVAISPS
AWYSWCSQRLVEERYSWTSQLSPADLIPLEVPTWQEQLVVGHNVSFDRAH
IREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKAISSWDWLDIS
SVNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVW
ATHEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAEAQGT
YEELQREMKKSLMDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQKKPC
SEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLCPRLDDP
AWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPGRVVCPYR
AIESLYRKHCLEQYHHGNGPYNDVDIPGCWFFKLPHKDGNSCNVGSPFAK
DFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMVVWLPR
SALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTASNARPD
RVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGCTAFGW
MTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIYGAGQPFAERLLMQ
FNHRLTQQEAAEKAQQMYAATWKGGTESEMFNKLESIATSDIPRTPVLGC
CISRALEPSAVQEEFMTSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDG
RFCISIHDEVRYLVREEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSV
AFFSAVDIDRCLRKEVTMDCKTPSNPTGMERRYGIPQGEALDIYQIIELT
KGSLEKRS
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain8d3r Chain A Residue 1302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8d3r Pol gamma coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.
Resolution3.04 Å
Binding residue
(original residue number in PDB)		D890 D1135
Binding residue
(residue number reindexed from 1)		D672 D858
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-
4.2.99.-
Gene Ontology
Molecular Function
GO:0002020 protease binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005515 protein binding
GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity
GO:0008408 3'-5' exonuclease activity
GO:0016787 hydrolase activity
GO:0016829 lyase activity
GO:0051575 5'-deoxyribose-5-phosphate lyase activity
Biological Process
GO:0006259 DNA metabolic process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006264 mitochondrial DNA replication
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006287 base-excision repair, gap-filling
GO:0045004 DNA replication proofreading
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0000262 mitochondrial chromosome
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005760 gamma DNA polymerase complex
GO:0032991 protein-containing complex
GO:0042645 mitochondrial nucleoid
GO:0043231 intracellular membrane-bounded organelle

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8d3r, PDBe:8d3r, PDBj:8d3r
PDBsum8d3r
PubMed37202477
UniProtP54098|DPOG1_HUMAN DNA polymerase subunit gamma-1 (Gene Name=POLG)

[Back to BioLiP]