SMTL ID : 6k1e.1

Crystal structure of EXD2 exonuclease domain soaked in Mg and GMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: D.33 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.33, H2O.1, H2O.1, H2O.1, H2O.1 MG.2: 4 residues within 4Å: Chain A: D.33, E.35 Chain B: Y.167, D.171 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.171, A:D.33, A:E.35, H2O.1, H2O.1 MG.3: 4 residues within 4Å: Chain A: Y.167, D.171 Chain B: D.33, E.35 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.171, B:D.33, B:E.35, H2O.1 MG.4: 1 residues within 4Å: Chain B: D.33 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.33, H2O.1, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., The structure of human EXD2 reveals a chimeric 3' to 5' exonuclease domain that discriminates substrates via metal coordination. Nucleic Acids Res. (2019)

Release Date

2019-05-22

Peptides

Exonuclease 3'-5' domain-containing protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Exonuclease 3'-5' domain-containing protein 2

Related Entries With Identical Sequence