Loading
PDBj
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help

4RQ7

Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dATP soaked with MgCl2 for 1hr

Functional Information from GO Data
ChainGOidnamespacecontents
A0001701biological_processin utero embryonic development
A0003677molecular_functionDNA binding
A0003684molecular_functiondamaged DNA binding
A0003887molecular_functionDNA-directed DNA polymerase activity
A0003906molecular_functionDNA-(apurinic or apyrimidinic site) endonuclease activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005737cellular_componentcytoplasm
A0005874cellular_componentmicrotubule
A0005876cellular_componentspindle microtubule
A0006260biological_processDNA replication
A0006261biological_processDNA-templated DNA replication
A0006281biological_processDNA repair
A0006284biological_processbase-excision repair
A0006287biological_processbase-excision repair, gap-filling
A0006290biological_processpyrimidine dimer repair
A0006297biological_processnucleotide-excision repair, DNA gap filling
A0006303biological_processdouble-strand break repair via nonhomologous end joining
A0006915biological_processapoptotic process
A0006954biological_processinflammatory response
A0006974biological_processDNA damage response
A0007435biological_processsalivary gland morphogenesis
A0008017molecular_functionmicrotubule binding
A0008630biological_processintrinsic apoptotic signaling pathway in response to DNA damage
A0010332biological_processresponse to gamma radiation
A0016445biological_processsomatic diversification of immunoglobulins
A0016446biological_processsomatic hypermutation of immunoglobulin genes
A0016740molecular_functiontransferase activity
A0016779molecular_functionnucleotidyltransferase activity
A0016829molecular_functionlyase activity
A0019899molecular_functionenzyme binding
A0032991cellular_componentprotein-containing complex
A0034061molecular_functionDNA polymerase activity
A0045471biological_processresponse to ethanol
A0046872molecular_functionmetal ion binding
A0048535biological_processlymph node development
A0048536biological_processspleen development
A0048872biological_processhomeostasis of number of cells
A0051402biological_processneuron apoptotic process
A0051575molecular_function5'-deoxyribose-5-phosphate lyase activity
A0055093biological_processresponse to hyperoxia
A0071707biological_processimmunoglobulin heavy chain V-D-J recombination
A0071897biological_processDNA biosynthetic process
A0140078molecular_functionclass I DNA-(apurinic or apyrimidinic site) endonuclease activity
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA A 401
ChainResidue
ATHR101
AVAL103
AILE106
PDG9
PHOH201
PHOH202

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA A 402
ChainResidue
AHOH549
DDC3
DHOH202
ALYS60
ALEU62
AVAL65

site_idAC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL A 403
ChainResidue
AASN294
ATHR297
AARG299

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CL A 404
ChainResidue
AALA32
AILE33
AHIS34
ALYS35
AHOH546
DHOH206

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA D 101
ChainResidue
DHOH205
DHOH211
TACT102
THOH205
THOH233

site_idAC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE ACT P 101
ChainResidue
PDT3
PDG4

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA T 101
ChainResidue
THOH222
THOH223
THOH224
THOH227
THOH231

site_idAC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ACT T 102
ChainResidue
DNA101
DHOH211
TDG3
TDA4
THOH205
THOH233

Functional Information from PROSITE/UniProt
site_idPS00522
Number of Residues20
DetailsDNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP
ChainResidueDetails
AGLY179-PRO198

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues9
DetailsRegion: {"description":"DNA-binding"}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues1
DetailsActive site: {"description":"Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity","evidences":[{"source":"PubMed","id":"9572863","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12517346","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8841120","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9287163","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1BPX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1BPZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1MQ3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ZQO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ZQQ","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"8841119","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8ICW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8ICX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8ICY","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"8841119","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8ICX","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"9287163","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1BPY","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q8K409","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"Omega-N-methylarginine; by PRMT6","evidences":[{"source":"PubMed","id":"16600869","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"19713937","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21362556","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

239149

PDB entries from 2025-07-23

PDB statisticsPDBj update infoContact PDBjnumon