SMTL ID : 6k1a.1

Crystal structure of EXD2 exonuclease domain soaked in Mn and Mg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 3 residues within 4Å: Chain A: D.33, E.35 Chain B: D.171 6 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.33, A:E.35, B:D.171, H2O.1, H2O.1, H2O.2 MN.3: 4 residues within 4Å: Chain A: D.171 Chain B: D.33, E.35 Ligands: MG.4 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.33, B:E.35, A:D.171, H2O.2, H2O.2

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.33 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.33, H2O.1, H2O.1 MG.4: 2 residues within 4Å: Chain B: D.33 Ligands: MN.3 No protein-ligand interaction detected (PLIP)

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

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