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4DOC

Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer

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
A0009059biological_processmacromolecule biosynthetic process
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 Residues4
DetailsBINDING SITE FOR RESIDUE MG A 401
ChainResidue
AASP190
AASP192
AG1C410
AHOH501

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE NA A 402
ChainResidue
AASP190
AASP192
AASP256
AG1C410

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA A 403
ChainResidue
AVAL103
AILE106
PDG9
PHOH101
PHOH115
ATHR101

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA A 404
ChainResidue
ALYS60
ALEU62
AVAL65
AHOH812
DDC3

site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE CL A 405
ChainResidue
AGLN264
ATYR266
ACYS267
AVAL313

site_idAC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL A 406
ChainResidue
AALA32
AHIS34
ALYS35

site_idAC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL A 407
ChainResidue
ALEU82
AARG89
AHOH729

site_idAC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE CL A 408
ChainResidue
AASN294
ATHR297
AARG299
AHOH702

site_idAC9
Number of Residues2
DetailsBINDING SITE FOR RESIDUE CL A 409
ChainResidue
APRO330
ALYS331

site_idBC1
Number of Residues26
DetailsBINDING SITE FOR RESIDUE G1C A 410
ChainResidue
AGLY179
ASER180
AARG183
ASER188
AGLY189
AASP190
AASP192
ATYR271
APHE272
ATHR273
AGLY274
AASP276
AASN279
AARG283
AMG401
ANA402
AHOH501
AHOH503
AHOH523
AHOH595
AHOH633
AHOH716
AHOH719
PDOC10
TDC6
TDG7

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 Residues1
DetailsACT_SITE: Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269|PubMed:9572863
ChainResidueDetails
ALYS72

site_idSWS_FT_FI2
Number of Residues6
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
ALYS60
ALEU62
AVAL65
ATHR101
AVAL103
AILE106

site_idSWS_FT_FI3
Number of Residues3
DetailsBINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
ChainResidueDetails
AARG149
ASER180
AGLY189

site_idSWS_FT_FI4
Number of Residues1
DetailsBINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX
ChainResidueDetails
AARG183

site_idSWS_FT_FI5
Number of Residues3
DetailsBINDING: BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
ChainResidueDetails
AASP190
AASP192
AASP256

site_idSWS_FT_FI6
Number of Residues1
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409
ChainResidueDetails
ALYS72

site_idSWS_FT_FI7
Number of Residues2
DetailsMOD_RES: Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869
ChainResidueDetails
AARG83
AARG152

site_idSWS_FT_FI8
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556
ChainResidueDetails
ALYS41
ALYS61
ALYS81

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PDB entries from 2024-03-27

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