SMTL ID : 4qh9.1

Crystal structure of Mn2+ bound human APE1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: K.194, K.195, P.201 No protein-ligand interaction detected (PLIP) EDO.2: 4 residues within 4Å: Chain A: S.82, H.83, Q.84, Y.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.84, A:Q.84 EDO.3: 4 residues within 4Å: Chain A: P.215, S.255, H.256, S.257 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.215, A:H.256, A:S.257, A:S.257 Water bridges: A:S.257 EDO.4: 5 residues within 4Å: Chain A: H.182, E.183, R.204, Q.205, G.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.183 EDO.5: 7 residues within 4Å: Chain A: L.29, D.57, I.58, S.102, R.103, Q.104, F.129 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.103, A:Q.104, A:Q.104, A:Q.104 EDO.6: 2 residues within 4Å: Chain A: K.45, Y.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.45 EDO.7: 5 residues within 4Å: Chain A: A.105, P.106, L.107, F.129, D.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.105, A:D.130, A:D.130 Water bridges: A:A.105

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

MN.8: 2 residues within 4Å: Chain A: D.37, E.63 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.37, A:E.63, H2O.4, H2O.4, H2O.4, H2O.4

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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