SMTL ID : 4iem.2 (3 other biounits)

Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

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

DG-DC-DT-DA-DC.1: 18 residues within 4Å: Chain A: E.95, K.124, Y.127, R.155, Y.170, N.173, G.175, R.176, R.180, N.211 Chain B: G.6, G.7, T.8, A.9, G.10, C.11 Ligands: 3DR-DG-DA-DT-DC.2, MG.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.178 Hydrogen bonds: A:R.72, A:A.73, A:K.97, A:G.177, A:K.227, A:M.270 Water bridges: A:R.72, A:R.72, A:R.72, A:R.176, A:R.176 Salt bridges: A:R.72, A:K.77

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

3DR-DG-DA-DT-DC.2: 28 residues within 4Å: Chain A: N.67, E.95, Y.170, N.173, R.176, D.209, N.211, N.221, N.225, N.228, A.229, G.230, F.265, T.267, M.269, M.270, A.272, V.277, W.279, L.281, H.308 Chain B: G.2, A.3, T.4, C.5, G.6 Ligands: DG-DC-DT-DA-DC.1, MG.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.265, A:W.279 Hydrogen bonds: A:E.95, A:Y.170, A:N.173, A:N.211, A:N.228 Salt bridges: A:H.308

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: N.67, E.95, Y.170, H.308 Ligands: DG-DC-DT-DA-DC.1, 3DR-DG-DA-DT-DC.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.95, H2O.1, H2O.1, H2O.1

3 x NA: SODIUM ION(Non-functional Binders)

NA.4: 7 residues within 4Å: Chain A: D.46, P.47, F.252, Y.256, D.296, S.297, K.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.256, A:D.296, A:K.298 NA.5: 6 residues within 4Å: Chain A: R.184, D.188, V.212, E.235, G.238, F.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.184, A:R.184, A:D.188 NA.6: 4 residues within 4Å: Chain A: D.188, F.191, R.192, L.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.192, A:G.238

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

DNA-(apurinic or apyrimidinic site) lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA-(apurinic or apyrimidinic site) lyase

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