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6UOK

Y271G DNA polymerase beta substrate complex with templating cytosine and incoming r8-oxo-GTP

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
A0006259biological_processDNA metabolic process
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
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
F0001701biological_processin utero embryonic development
F0003677molecular_functionDNA binding
F0003684molecular_functiondamaged DNA binding
F0003887molecular_functionDNA-directed DNA polymerase activity
F0003906molecular_functionDNA-(apurinic or apyrimidinic site) endonuclease activity
F0005515molecular_functionprotein binding
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005737cellular_componentcytoplasm
F0005874cellular_componentmicrotubule
F0005876cellular_componentspindle microtubule
F0006259biological_processDNA metabolic process
F0006260biological_processDNA replication
F0006261biological_processDNA-templated DNA replication
F0006281biological_processDNA repair
F0006284biological_processbase-excision repair
F0006287biological_processbase-excision repair, gap-filling
F0006290biological_processpyrimidine dimer repair
F0006297biological_processnucleotide-excision repair, DNA gap filling
F0006303biological_processdouble-strand break repair via nonhomologous end joining
F0006915biological_processapoptotic process
F0006954biological_processinflammatory response
F0006974biological_processDNA damage response
F0007435biological_processsalivary gland morphogenesis
F0008017molecular_functionmicrotubule binding
F0008630biological_processintrinsic apoptotic signaling pathway in response to DNA damage
F0010332biological_processresponse to gamma radiation
F0016445biological_processsomatic diversification of immunoglobulins
F0016446biological_processsomatic hypermutation of immunoglobulin genes
F0016779molecular_functionnucleotidyltransferase activity
F0016829molecular_functionlyase activity
F0019899molecular_functionenzyme binding
F0032991cellular_componentprotein-containing complex
F0034061molecular_functionDNA polymerase activity
F0045471biological_processresponse to ethanol
F0046872molecular_functionmetal ion binding
F0048535biological_processlymph node development
F0048536biological_processspleen development
F0048872biological_processhomeostasis of number of cells
F0051402biological_processneuron apoptotic process
F0051575molecular_function5'-deoxyribose-5-phosphate lyase activity
F0055093biological_processresponse to hyperoxia
F0071707biological_processimmunoglobulin heavy chain V-D-J recombination
F0071897biological_processDNA biosynthetic process
F0140078molecular_functionclass I DNA-(apurinic or apyrimidinic site) endonuclease activity
Functional Information from PDB Data
site_idAC1
Number of Residues1
Detailsbinding site for residue CL B 101
ChainResidue
BDG3

site_idAC2
Number of Residues4
Detailsbinding site for residue NA E 101
ChainResidue
EDC3
FLYS60
FLEU62
FVAL65

site_idAC3
Number of Residues5
Detailsbinding site for residue NA F 401
ChainResidue
FHOH513
CDG9
FTHR101
FVAL103
FILE106

site_idAC4
Number of Residues4
Detailsbinding site for residue MN F 402
ChainResidue
FASP190
FASP192
F8GT406
FHOH507

site_idAC5
Number of Residues2
Detailsbinding site for residue MN F 403
ChainResidue
FASP145
FHIS252

site_idAC6
Number of Residues2
Detailsbinding site for residue MN F 404
ChainResidue
FASP124
FHOH501

site_idAC7
Number of Residues4
Detailsbinding site for residue NA F 405
ChainResidue
FASP190
FASP192
FASP256
F8GT406

site_idAC8
Number of Residues20
Detailsbinding site for residue 8GT F 406
ChainResidue
BDC6
BDG7
CDOC10
FGLY179
FSER180
FARG183
FSER188
FGLY189
FASP190
FASP192
FGLY271
FPHE272
FTHR273
FGLY274
FASP276
FASN279
FMN402
FNA405
FMN408
FHOH507

site_idAC9
Number of Residues2
Detailsbinding site for residue MN F 407
ChainResidue
FASP314
FASP318

site_idAD1
Number of Residues1
Detailsbinding site for residue MN F 408
ChainResidue
F8GT406

site_idAD2
Number of Residues1
Detailsbinding site for residue EDO A 401
ChainResidue
AHIS51

site_idAD3
Number of Residues5
Detailsbinding site for residue NA A 402
ChainResidue
ALYS60
ALEU62
AVAL65
AHOH517
DDC3

site_idAD4
Number of Residues5
Detailsbinding site for residue NA A 403
ChainResidue
ATHR101
AVAL103
AILE106
AHOH519
PDG9

site_idAD5
Number of Residues4
Detailsbinding site for residue MN A 404
ChainResidue
AASP190
AASP192
A8GT405
AHOH515

site_idAD6
Number of Residues15
Detailsbinding site for residue 8GT A 405
ChainResidue
AARG149
AGLY179
ASER180
ASER188
AGLY189
AASP190
AASP192
APHE272
AASP276
AMN404
ANA406
AHOH515
PDOC10
TDC6
TDG7

site_idAD7
Number of Residues4
Detailsbinding site for residue NA A 406
ChainResidue
AASP190
AASP192
AASP256
A8GT405

site_idAD8
Number of Residues1
Detailsbinding site for residue MG D 101
ChainResidue
DDG4

site_idAD9
Number of Residues11
Detailsbinding site for Di-nucleotide DG P 9 and DOC P 10
ChainResidue
AVAL103
AGLY105
AILE106
AARG254
ANA403
A8GT405
PDC8
TDC6
TDG7
TDC8
TDG9

Functional Information from PROSITE/UniProt
site_idPS00522
Number of Residues20
DetailsDNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP
ChainResidueDetails
FGLY179-PRO198

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269|PubMed:9572863
ChainResidueDetails
FLYS72
ALYS72

site_idSWS_FT_FI2
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
ChainResidueDetails
FLYS60
ATHR101
AVAL103
AILE106
FLEU62
FVAL65
FTHR101
FVAL103
FILE106
ALYS60
ALEU62
AVAL65

site_idSWS_FT_FI3
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
ChainResidueDetails
FARG149
FSER180
FGLY189
AARG149
ASER180
AGLY189

site_idSWS_FT_FI4
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX
ChainResidueDetails
FARG183
AARG183

site_idSWS_FT_FI5
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
ChainResidueDetails
FASP190
FASP192
FASP256
AASP190
AASP192
AASP256

site_idSWS_FT_FI6
Number of Residues2
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409
ChainResidueDetails
FLYS72
ALYS72

site_idSWS_FT_FI7
Number of Residues4
DetailsMOD_RES: Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869
ChainResidueDetails
FARG83
FARG152
AARG83
AARG152

site_idSWS_FT_FI8
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556
ChainResidueDetails
FLYS41
FLYS61
FLYS81
ALYS41
ALYS61
ALYS81

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PDB entries from 2024-07-24

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