SMTL ID : 9mbj.1

8-Oxo-dGTP hydrolysis in human MTH1(G2K mutant) crystal using Mn2+: the EP-M complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

2 x 8OG: 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

8OG.1: 16 residues within 4Å: Chain A: Y.7, T.8, L.9, K.23, F.27, N.33, G.36, G.37, E.56, F.72, M.81, W.117, D.119, D.120, W.123 Ligands: MN.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.33, A:N.33, A:G.36 Water bridges: A:K.23, A:K.23, A:F.27, A:K.38 Salt bridges: A:K.23, A:D.119, A:D.120 pi-Stacking: A:W.117, A:W.117 8OG.5: 17 residues within 4Å: Chain B: Y.7, T.8, L.9, K.23, F.27, N.33, G.36, G.37, E.56, F.72, M.81, W.117, D.119, D.120, W.123 Ligands: MN.6, MN.8 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.33, B:N.33, B:G.36, B:K.38 Salt bridges: B:K.23, B:D.119, B:D.120 pi-Stacking: B:W.117, B:W.117

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

MN.2: 4 residues within 4Å: Chain A: G.36, E.56 Ligands: 8OG.1, MN.3 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.36, A:E.56, H2O.2, H2O.3, H2O.3 MN.3: 6 residues within 4Å: Chain A: G.36, E.52, E.56, E.100 Ligands: MN.2, MN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.52, A:E.56, A:E.100, H2O.3 MN.4: 3 residues within 4Å: Chain A: R.51, E.52 Ligands: MN.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.52, H2O.1, H2O.2 MN.6: 4 residues within 4Å: Chain B: G.36, E.56 Ligands: 8OG.5, MN.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.36, B:E.56, H2O.6, H2O.8 MN.7: 2 residues within 4Å: Chain B: E.52 Ligands: MN.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.52, H2O.6, H2O.8 MN.8: 6 residues within 4Å: Chain B: G.36, E.52, E.56 Ligands: 8OG.5, MN.6, MN.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.52, B:E.56, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirata, K. et al., Neutron and time-resolved X-ray crystallography reveal the substrate recognition and catalytic mechanism of human Nudix hydrolase MTH1. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-07-30

Peptides

7,8-dihydro-8-oxoguanine triphosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

7,8-dihydro-8-oxoguanine triphosphatase

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