SMTL ID : 5dg0.1 (1 other biounit)

Human APE1 phosphorothioate substrate complex with Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.1: 3 residues within 4Å: Chain A: D.28, E.54, D.266 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.28, A:E.54, H2O.1, H2O.1, H2O.2 MN.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MN.3: 3 residues within 4Å: Chain A: G.183, N.187 Chain B: G.13 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.183 MN.9: 1 residues within 4Å: Chain B: G.1 No protein-ligand interaction detected (PLIP) MN.10: 1 residues within 4Å: Chain B: G.4 No protein-ligand interaction detected (PLIP) MN.11: 2 residues within 4Å: Chain B: C.15, G.16 No protein-ligand interaction detected (PLIP)

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

EDO.4: 7 residues within 4Å: Chain A: V.130, W.146, D.147, F.150, L.169, G.197, F.198 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.143, A:D.147, A:R.151, A:L.201 EDO.5: 5 residues within 4Å: Chain A: L.2, Y.3, W.225, R.232, N.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.3, A:Y.3, A:R.232 EDO.6: 2 residues within 4Å: Chain A: G.136, L.137 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.136, A:E.141 EDO.7: 7 residues within 4Å: Chain A: F.224, T.226, Y.227, D.266 Chain B: C.10, C.12 Chain C: G.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.135, A:Y.227

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 4 residues within 4Å: Chain A: E.59, Y.76, W.77, Y.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Freudenthal, B.D. et al., Capturing snapshots of APE1 processing DNA damage. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-10-14

Peptides

DNA-(apurinic or apyrimidinic site) lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-(apurinic or apyrimidinic site) lyase

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