SMTL ID : 4qhe.1

Crystal structure of Mg2+ bound human APE1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.37, E.63 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.37, A:E.63, H2O.1, H2O.1, H2O.3

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

EDO.2: 5 residues within 4Å: Chain A: H.182, E.183, R.204, Q.205, G.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.183, A:G.208 EDO.3: 6 residues within 4Å: Chain A: P.79, G.80, S.82, H.83, S.102, R.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.80, A:S.82, A:S.82 EDO.4: 7 residues within 4Å: Chain A: D.156, F.159, R.160, G.206, E.209, L.210 Ligands: EDO.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.156, A:R.160, A:R.160, A:E.209, A:E.209 EDO.5: 4 residues within 4Å: Chain A: S.82, H.83, Q.84, Y.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.84, A:Q.84, A:Y.85 EDO.6: 9 residues within 4Å: Chain A: V.139, W.155, D.156, F.159, L.178, G.206, F.207, L.210 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.155, A:D.156, A:G.206 Water bridges: A:R.152 EDO.7: 1 residues within 4Å: Chain A: E.184 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, H. et al., High-resolution crystal structures reveal plasticity in the metal binding site of apurinic/apyrimidinic endonuclease I. Biochemistry (2014)

Release Date

2014-11-12

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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