SMTL ID : 4hno.1

High resolution crystal structure of DNA Apurinic/apyrimidinic (AP) endonuclease IV Nfo from Thermatoga maritima

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.92 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 11 residues within 4Å: Chain A: H.72, Y.75, N.110, H.112, E.147, H.184, H.218 Ligands: MN.4, ZN.5, TRS.7, EDO.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.72, A:H.112, A:E.147, A:E.147, H2O.15 ZN.3: 6 residues within 4Å: Chain A: H.184, D.231, H.233 Ligands: MN.2, TRS.7, EDO.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.184, A:D.231, A:H.233 ZN.5: 11 residues within 4Å: Chain A: E.147, D.181, H.184, H.218, N.220, H.233, E.263 Ligands: ZN.1, MN.4, TRS.7, EDO.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.147, A:D.181, A:H.218, A:E.263, H2O.15

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: H.184, D.231, H.233 Ligands: ZN.3, TRS.7, EDO.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.184, A:D.231, A:D.231, A:H.233 MN.4: 11 residues within 4Å: Chain A: E.147, D.181, H.184, H.218, N.220, H.233, E.263 Ligands: ZN.1, ZN.5, TRS.7, EDO.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.147, A:D.181, A:H.218, A:E.263, H2O.15

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.6: 1 residues within 4Å: Chain A: S.48 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 14 residues within 4Å: Chain A: Y.75, H.112, E.147, D.181, H.184, D.231, H.233, E.263 Ligands: ZN.1, MN.2, ZN.3, MN.4, ZN.5, EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.75, A:D.231 Water bridges: A:Y.75

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 11 residues within 4Å: Chain A: Y.75, H.112, H.184, D.231, H.233 Ligands: ZN.1, MN.2, ZN.3, MN.4, ZN.5, TRS.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.231 EDO.9: 6 residues within 4Å: Chain A: F.186, D.191, T.193, K.194, L.226, F.240 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.240

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 3 residues within 4Å: Chain A: E.50, K.54, R.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsutakawa, S.E. et al., Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes. J.Biol.Chem. (2013)

Release Date

2013-01-23

Peptides

Probable endonuclease 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Probable endonuclease 4