SMTL ID : 7n3y.1 (1 other biounit)

Crystal Structure of Saccharomyces cerevisiae Apn2 Catalytic Domain E59Q/D222N Mutant in Complex with DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

homo-dimer

Ligands

1 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.1: 6 residues within 4Å: Chain A: R.196, N.224, V.225, C.226, H.271, R.272 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.224, A:C.226, A:R.272 Water bridges: A:R.196 Salt bridges: A:R.196, A:H.271, A:R.272

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: K.12, D.53 No protein-ligand interaction detected (PLIP)

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.3: 7 residues within 4Å: Chain B: R.196, N.224, V.225, C.226, H.271, R.272, S.325 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:C.226, B:R.272, B:S.325 Salt bridges: B:R.196, B:H.271, B:R.272

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 7 residues within 4Å: Chain B: Y.89, R.165, Y.181, P.183, A.184, N.185, S.186 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.89 Hydrogen bonds: B:Q.59, B:Y.89, B:A.184, B:N.185, B:S.186, B:S.186, B:S.186, B:S.186, B:S.186 Water bridges: B:S.90 Salt bridges: B:R.165, B:R.165

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

EDO.5: 4 residues within 4Å: Chain B: S.156, E.159, L.160, R.198 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.156, B:R.198, B:R.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, J.S. et al., Molecular basis for processing of topoisomerase 1-triggered DNA damage by Apn2/APE2. Cell Rep (2022)

Release Date

2022-09-28

Peptides

DNA-(apurinic or apyrimidinic site) endonuclease 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA-(apurinic or apyrimidinic site) endonuclease 2

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