SMTL ID : 7x9o.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 5 residues within 4Å: Chain A: E.47, H.64, F.65, S.66 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.67, A:E.47 Hydrogen bonds: A:H.64, A:F.65

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

8OG.2: 15 residues within 4Å: Chain A: I.6, V.8, R.23, H.28, E.34, F.35, G.37, G.38, F.75, I.80, L.82, P.116, A.118, N.119 Ligands: MG.4 17 PLIP interactions: 17 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:G.37, A:G.37, A:G.37, A:K.39, A:E.57, A:E.57 Salt bridges: A:R.23, A:E.34

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

SO4.3: 4 residues within 4Å: Chain A: Q.63, H.64, F.65 Ligands: GLC-FRU.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.64

2 x MG: MAGNESIUM ION(Non-covalent)

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

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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