SMTL ID : 4k1g.2 (1 other biounit)

Structure of E. coli Nfo(Endo IV)-H69A mutant bound to a cleaved DNA duplex containing a alphadA:T basepair

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x DG- DC- DG- DT- DC- DC: DNA (5'-D(*GP*CP*GP*TP*CP*C)-3')(Non-covalent)

DG-DC-DG-DT-DC-DC.1: 18 residues within 4Å: Chain A: H.7, F.32, R.37, A.69, Y.72, H.109, H.182, D.229, R.230, H.231, E.261, I.263 Chain B: G.11, A.12, C.13, G.14, C.15 Ligands: ZN.4 Protein-ligand interaction information (PLIP) not available

1 x DA- DC- DG- DA- DC- DG- DA- DC: DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3')(Non-covalent)

DA-DC-DG-DA-DC-DG-DA-DC.2: 15 residues within 4Å: Chain A: S.9, A.11, G.12, N.35, Q.36, R.37, Q.38 Chain B: G.2, T.3, C.4, G.5, T.6, C.7, G.8, T.9 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:W.39, A:Y.72, A:R.230 Water bridges: A:W.39, A:R.40, A:K.86, A:R.230, A:R.230

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: E.145, D.179, H.182, H.216, E.261 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.145, A:D.179, A:H.216, A:E.261, H2O.3 ZN.4: 5 residues within 4Å: Chain A: H.182, D.229, H.231 Ligands: DG-DC-DG-DT-DC-DC.1, DG-DC-DG-DT-DC-DC.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.182, A:D.229, A:D.229, A:H.231

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: A.204, R.205, T.206, V.207, G.208, K.210 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazouzi, A. et al., Insight into mechanisms of 3'-5' exonuclease activity and removal of bulky 8,5'-cyclopurine adducts by apurinic/apyrimidinic endonucleases. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-07-31

Peptides

Endonuclease 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Endonuclease 4

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