SMTL ID : 5zyw.1

The crystal structure of apo-HsMGME1 with Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: L.146, D.148, E.254 Ligands: MN.2, TLA.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.148, A:E.254, H2O.1, H2O.2, H2O.3 MN.2: 6 residues within 4Å: Chain A: H.90, D.148, D.161, W.162 Ligands: MN.1, TLA.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.90, A:D.148, A:D.161, A:W.162 MN.3: 3 residues within 4Å: Chain A: T.44, K.169, S.253 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.44, A:S.253, H2O.1, H2O.2

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

TLA.4: 13 residues within 4Å: Chain A: T.44, H.90, D.148, D.161, W.162, K.163, P.168, K.169, Q.173, Q.181, E.254 Ligands: MN.1, MN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.163, A:Q.173, A:Q.181 Water bridges: A:H.90, A:H.90, A:E.254 Salt bridges: A:H.90, A:K.163, A:K.169

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: T.175, N.178, P.179, I.204, V.206, H.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.178

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

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