SMTL ID : 5zyv.1

Crystal structure of human MGME1 with single strand DNA2 and Ca2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.148, D.161, W.162 Ligands: ACT.3 6 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.148, A:D.161, A:W.162, H2O.1, H2O.1, ACT.3 CA.2: 4 residues within 4Å: Chain A: M.189, N.190, D.192, Y.195 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.192, A:Y.195

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 8 residues within 4Å: Chain A: L.146, D.148, D.161, Q.181, Y.185 Chain B: A.4, A.5 Ligands: CA.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.181, A:Y.185, A:Y.185 Salt bridges: A:K.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, C. et al., Structural insights into DNA degradation by human mitochondrial nuclease MGME1. Nucleic Acids Res. (2018)

Release Date

2018-09-19

Peptides

Mitochondrial genome maintenance exonuclease 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mitochondrial genome maintenance exonuclease 1