SMTL ID : 2nq9.1

High resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) Y72A mutant bound to damaged DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x DA- DT- DA- DT- DC- DT: 5'-D(*AP*TP*AP*TP*CP*T)-3'(Non-covalent)

DA-DT-DA-DT-DC-DT.1: 12 residues within 4Å: Chain A: A.6, A.7, G.8, T.9, A.10, T.11 Chain B: D.229, R.230, H.231 Ligands: 3DR-DA-DG-DA-DT.2, 3DR-DA-DG-DA-DT.2, ZN.5 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:N.35, B:R.37, B:W.39, B:N.75, B:G.151, B:S.152, B:N.153, B:R.230 Water bridges: B:R.37, B:R.37, B:R.37, B:R.37, B:R.37, B:R.37, B:Q.150, B:Q.150, B:S.152, B:R.230 Salt bridges: B:H.78

1 x 3DR- DA- DG- DA- DT: 5'-D(P*(3DR)P*AP*GP*AP*T)-3'(Non-covalent)

3DR-DA-DG-DA-DT.2: 26 residues within 4Å: Chain A: A.1, T.2, C.3, T.4 Chain B: H.7, S.9, A.10, A.11, G.12, F.32, N.35, Q.36, R.37, Q.38, H.69, H.109, E.145, D.179, H.182, H.216, H.231, E.261 Ligands: DA-DT-DA-DT-DC-DT.1, ZN.3, ZN.4, ZN.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.32 Salt bridges: B:H.69, B:H.109, B:H.182, B:H.216, B:H.231

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain B: H.69, N.107, H.109, E.145, H.216 Ligands: 3DR-DA-DG-DA-DT.2, ZN.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.69, B:H.109, B:E.145 ZN.4: 7 residues within 4Å: Chain B: E.145, D.179, H.182, H.216, E.261 Ligands: 3DR-DA-DG-DA-DT.2, ZN.3 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.145, B:D.179, B:H.216, B:E.261 ZN.5: 5 residues within 4Å: Chain B: H.182, D.229, H.231 Ligands: DA-DT-DA-DT-DC-DT.1, 3DR-DA-DG-DA-DT.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.182, B:D.229, B:D.229, B:H.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcin, E.D. et al., DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat.Struct.Mol.Biol. (2008)

Release Date

2007-11-13

Peptides

Endonuclease 4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

Endonuclease 4