Structure of PDB 2bpg Chain B Binding Site BS01

Receptor Information
>2bpg Chain B (length=324) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAE
AKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGP
SAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQM
QDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQP
KLLHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSENEYPHRRIDIRLIP
KDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPL
PVDSEQDIFDYIQWRYREPKDRSE
Ligand information
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]
PDB2bpg Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		S229 K230 G231 E232 T233 K234 R258 R283 N294 E295 Y296
Binding residue
(residue number reindexed from 1)		S221 K222 G223 E224 T225 K226 R247 R272 N283 E284 Y285
Enzymatic activity
Catalytic site (original residue number in PDB) D190 D192 D256
Catalytic site (residue number reindexed from 1) D182 D184 D245
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
4.2.99.-
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0016779 nucleotidyltransferase activity
GO:0016829 lyase activity
GO:0019899 enzyme binding
GO:0034061 DNA polymerase activity
GO:0046872 metal ion binding
GO:0051575 5'-deoxyribose-5-phosphate lyase activity
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological Process
GO:0001701 in utero embryonic development
GO:0006259 DNA metabolic process
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006287 base-excision repair, gap-filling
GO:0006290 pyrimidine dimer repair
GO:0006297 nucleotide-excision repair, DNA gap filling
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006915 apoptotic process
GO:0006954 inflammatory response
GO:0006974 DNA damage response
GO:0007435 salivary gland morphogenesis
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010332 response to gamma radiation
GO:0016445 somatic diversification of immunoglobulins
GO:0016446 somatic hypermutation of immunoglobulin genes
GO:0045471 response to ethanol
GO:0048535 lymph node development
GO:0048536 spleen development
GO:0048872 homeostasis of number of cells
GO:0051402 neuron apoptotic process
GO:0055093 response to hyperoxia
GO:0071707 immunoglobulin heavy chain V-D-J recombination
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005874 microtubule
GO:0005876 spindle microtubule
GO:0032991 protein-containing complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2bpg, PDBe:2bpg, PDBj:2bpg
PDBsum2bpg
PubMed7516580
UniProtP06766|DPOLB_RAT DNA polymerase beta (Gene Name=Polb)

[Back to BioLiP]