PDB entry 2oq4

View 2oq4 on RCSB PDB site
Description: Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (E2Q) in complex with AP-site containing DNA substrate
Class: hydrolase/DNA
Keywords: Endonuclease VIII, oxidative damage, DNA repair, base excision, covalent intermediate, crystal structure, reaction mechanism, HYDROLASE/DNA COMPLEX
Deposited on 2007-01-31, released 2008-02-26
The last revision prior to the SCOPe 2.08 freeze date was dated 2009-02-24, with a file datestamp of 2009-02-03.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: 0.374
AEROSPACI score: 0.1 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Endonuclease VIII
    Species: Escherichia coli [TaxId:562]
    Gene: nei
    Database cross-references and differences (RAF-indexed):
    • Uniprot P50465 (0-261)
      • engineered (1)
      • see remark 999 (33)
      • see remark 999 (111)
    Domains in SCOPe 2.08: d2oq4a1, d2oq4a2, d2oq4a3
  • Chain 'B':
    Compound: Endonuclease VIII
    Species: Escherichia coli [TaxId:562]
    Gene: nei
    Database cross-references and differences (RAF-indexed):
    • Uniprot P50465 (0-261)
      • engineered (1)
      • see remark 999 (33)
      • see remark 999 (111)
    Domains in SCOPe 2.08: d2oq4b1, d2oq4b2, d2oq4b3
  • Chain 'C':
    Compound: 5'-d(*g*gp*cp*tp*tp*cp*ap*tp*cp*cp*tp*gp*g)-3'
  • Chain 'D':
    Compound: 5'-d(*c*cp*ap*gp*gp*ap*(ped)p*gp*ap*ap*gp*cp*c)-3'
  • Chain 'E':
    Compound: 5'-d(*g*gp*cp*tp*tp*cp*ap*tp*cp*cp*tp*gp*g)-3'
  • Chain 'F':
    Compound: 5'-d(*c*cp*ap*gp*gp*ap*(ped)p*gp*ap*ap*gp*cp*c)-3'
  • Heterogens: NA, ZN, SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2oq4A (A:)
pqgpeirraadnleaaikgkpltdvwfafpqlktyqsqligqhvthvetrgkallthfsn
dltlyshnqlygvwrvvdtgeepqttrvlrvklqtadktillysasdiemlrpeqltthp
flqrvgpdvldpnltpevvkerllsprfrnrqfagllldqaflaglgnylrveilwqvgl
tgnhkakdlnaaqldalahalleiprfsyatrgqvdenkhhgalfrfkvfhrdgepcerc
gsiiekttlssrpfywcpgcqh

    Sequence, based on observed residues (ATOM records): (download) 
    >2oq4A (A:)
pqgpeirraadnleaaikgkpltdvwfafpqlktyqsqligqhvthvetrgkallthfsn
dltlyshnqlygvwrvvdtgeepqttrvlrvklqtadktillysasdiemlrpeqltthp
flqrvgpdvldpnltpevvkerllsprfrnrqfagllldqaflaglgnylrveilwqvgl
tgnhkakdlnaaqldalahalleiprfsyatrglfrfkvfhrdgepcercgsiiekttls
srpfywcpgcqh

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2oq4B (B:)
pqgpeirraadnleaaikgkpltdvwfafpqlktyqsqligqhvthvetrgkallthfsn
dltlyshnqlygvwrvvdtgeepqttrvlrvklqtadktillysasdiemlrpeqltthp
flqrvgpdvldpnltpevvkerllsprfrnrqfagllldqaflaglgnylrveilwqvgl
tgnhkakdlnaaqldalahalleiprfsyatrgqvdenkhhgalfrfkvfhrdgepcerc
gsiiekttlssrpfywcpgcqh

    Sequence, based on observed residues (ATOM records): (download) 
    >2oq4B (B:)
pqgpeirraadnleaaikgkpltdvwfafpqlktyqsqligqhvthvetrgkallthfsn
dltlyshnqlygvwrvvdtgeepqttrvlrvklqtadktillysasdiemlrpeqltthp
flqrvgpdvldpnltpevvkerllsprfrnrqfagllldqaflaglgnylrveilwqvgl
tgnhkakdlnaaqldalahalleiprfsyatralfrfkvfhrdgepcercgsiiekttls
srpfywccqh

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.