SMTL ID : 7x9n.1

Crystal structure of MutT-8-oxo-dGTP complex with three Mg2+ ions: Reaction using Mg2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: Q.63, H.64, F.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.64 Water bridges: A:P.62, A:F.65, A:F.65

1 x 8DG: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

8DG.2: 21 residues within 4Å: Chain A: I.6, V.8, R.23, H.28, E.34, F.35, G.37, G.38, K.39, E.53, E.57, F.75, I.80, L.82, P.116, A.118, N.119 Ligands: 8OG.3, MG.4, MG.5, MG.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.23, A:F.35, A:F.35, A:F.35, A:K.39, A:N.119, A:N.119 Water bridges: A:R.23, A:R.23, A:G.37, A:K.39, A:R.52 Salt bridges: A:R.23, A:E.34, A:K.39

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

8OG.3: 17 residues within 4Å: Chain A: I.6, V.8, R.23, H.28, E.34, F.35, G.37, G.38, K.39, F.75, I.80, L.82, P.116, A.118, N.119 Ligands: 8DG.2, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.23, A:F.35, A:F.35, A:F.35, A:N.119, A:N.119 Water bridges: A:R.23, A:R.23, A:R.23, A:E.34, A:G.37, A:G.37, A:K.39 Salt bridges: A:R.23, A:E.34

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: G.37, G.38, E.57 Ligands: 8DG.2, 8OG.3, MG.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.37, A:E.57, H2O.1, H2O.2, H2O.2 MG.5: 3 residues within 4Å: Chain A: E.53 Ligands: 8DG.2, MG.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.53, H2O.1, H2O.1, H2O.4, H2O.5 MG.6: 6 residues within 4Å: Chain A: G.37, E.53, E.57 Ligands: 8DG.2, MG.4, MG.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.53, A:E.57, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakamura, T. et al., Visualization of mutagenic nucleotide processing by Escherichia coli MutT, a Nudix hydrolase. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-06-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

7,8-dihydro-8-oxoguanine-triphosphatase

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