SMTL ID : 3gsi.1

Crystal structure of D552A dimethylglycine oxidase mutant of Arthrobacter globiformis in complex with tetrahydrofolate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x THG: (6S)-5,6,7,8-TETRAHYDROFOLATE(Non-covalent)

THG.1: 17 residues within 4Å: Chain A: M.502, L.505, Y.536, A.549, I.550, T.551, G.563, A.564, N.565, Y.628, F.629, L.646, Y.648, E.655, Y.657, Y.696, F.716 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.629, A:L.646, A:Y.648, A:Y.696 Hydrogen bonds: A:T.551, A:T.551, A:T.551, A:G.563 Water bridges: A:Y.536, A:G.563, A:R.697, A:R.826 Salt bridges: A:E.655 pi-Stacking: A:Y.536 THG.4: 17 residues within 4Å: Chain B: M.502, L.505, Y.536, A.549, I.550, T.551, G.563, A.564, N.565, Y.628, F.629, L.646, Y.648, E.655, Y.657, Y.696, F.716 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.629, B:L.646, B:Y.648, B:Y.696 Hydrogen bonds: B:T.551, B:T.551, B:T.551, B:G.563 Water bridges: B:Y.536, B:G.563, B:R.697, B:R.826 Salt bridges: B:E.655 pi-Stacking: B:Y.536 THG.7: 17 residues within 4Å: Chain C: M.502, L.505, Y.536, A.549, I.550, T.551, G.563, A.564, N.565, Y.628, F.629, L.646, Y.648, E.655, Y.657, Y.696, F.716 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:F.629, C:L.646, C:Y.648, C:Y.696 Hydrogen bonds: C:T.551, C:T.551, C:G.563, C:Y.628, C:Y.657 Water bridges: C:Y.536, C:Y.536, C:G.563, C:E.655, C:E.655, C:R.697, C:R.826 Salt bridges: C:E.655 pi-Stacking: C:Y.536 THG.10: 17 residues within 4Å: Chain D: M.502, L.505, Y.536, A.549, I.550, T.551, G.563, A.564, N.565, Y.628, F.629, L.646, Y.648, E.655, Y.657, Y.696, F.716 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:F.629, D:L.646, D:Y.648, D:Y.696 Hydrogen bonds: D:T.551, D:T.551, D:G.563, D:Y.628, D:Y.657 Water bridges: D:Y.536, D:Y.536, D:G.563, D:E.655, D:E.655, D:R.697, D:R.826 Salt bridges: D:E.655 pi-Stacking: D:Y.536

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.254, V.409, D.413 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.254, A:V.409, H2O.16, H2O.16, H2O.16, H2O.16 MG.5: 3 residues within 4Å: Chain B: D.254, V.409, D.413 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.254, B:V.409, H2O.58, H2O.58, H2O.58, H2O.58 MG.8: 3 residues within 4Å: Chain C: D.254, V.409, D.413 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.254, C:V.409, H2O.99, H2O.99, H2O.100, H2O.100 MG.11: 3 residues within 4Å: Chain D: D.254, V.409, D.413 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.254, D:V.409, H2O.141, H2O.141, H2O.141, H2O.141

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.3: 34 residues within 4Å: Chain A: G.8, G.10, I.11, V.12, D.32, Q.33, P.39, G.41, S.42, T.43, H.45, A.46, P.47, G.48, L.49, T.169, T.170, V.171, C.199, A.200, G.201, W.203, I.207, H.222, Y.224, Y.256, F.328, G.330, I.331, F.332, V.357, W.358, V.359, T.360 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:P.47, A:Y.224, A:F.328, A:F.332 Hydrogen bonds: A:V.12, A:Q.33, A:Q.33, A:G.41, A:S.42, A:S.42, A:T.43, A:T.43, A:G.48, A:L.49, A:L.49, A:V.171, A:V.171, A:G.201, A:Y.256, A:V.359, A:T.360 Water bridges: A:G.10, A:G.10, A:P.39, A:G.40, A:G.40, A:F.202, A:F.202, A:V.357, A:T.360 pi-Stacking: A:W.203 FAD.6: 34 residues within 4Å: Chain B: G.8, G.10, I.11, V.12, D.32, Q.33, P.39, G.41, S.42, T.43, H.45, A.46, P.47, G.48, L.49, T.169, T.170, V.171, C.199, A.200, G.201, W.203, I.207, H.222, Y.224, Y.256, F.328, G.330, I.331, F.332, V.357, W.358, V.359, T.360 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:P.47, B:Y.224, B:F.328, B:F.332 Hydrogen bonds: B:V.12, B:Q.33, B:Q.33, B:G.41, B:S.42, B:S.42, B:T.43, B:T.43, B:G.48, B:L.49, B:L.49, B:V.171, B:V.171, B:G.201, B:Y.256, B:V.359, B:T.360 Water bridges: B:G.10, B:G.10, B:P.39, B:G.40, B:G.40, B:F.202, B:F.202, B:V.357, B:T.360 pi-Stacking: B:W.203 FAD.9: 34 residues within 4Å: Chain C: G.8, G.10, I.11, V.12, D.32, Q.33, P.39, G.41, S.42, T.43, H.45, A.46, P.47, G.48, L.49, T.169, T.170, V.171, C.199, A.200, G.201, W.203, I.207, H.222, Y.224, Y.256, F.328, G.330, I.331, F.332, V.357, W.358, V.359, T.360 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:P.47, C:Y.224, C:F.328, C:F.332 Hydrogen bonds: C:V.12, C:Q.33, C:Q.33, C:G.41, C:S.42, C:S.42, C:T.43, C:T.43, C:G.48, C:L.49, C:L.49, C:V.171, C:V.171, C:G.201, C:V.359, C:T.360, C:T.360 Water bridges: C:G.10, C:G.10, C:P.39, C:G.40, C:G.40, C:F.202, C:F.202, C:V.357 pi-Stacking: C:W.203 FAD.12: 34 residues within 4Å: Chain D: G.8, G.10, I.11, V.12, D.32, Q.33, P.39, G.41, S.42, T.43, H.45, A.46, P.47, G.48, L.49, T.169, T.170, V.171, C.199, A.200, G.201, W.203, I.207, H.222, Y.224, Y.256, F.328, G.330, I.331, F.332, V.357, W.358, V.359, T.360 30 PLIP interactions: 30 interactions with chain D Hydrophobic interactions: D:P.47, D:Y.224, D:F.328, D:F.332 Hydrogen bonds: D:V.12, D:Q.33, D:Q.33, D:G.41, D:S.42, D:S.42, D:T.43, D:T.43, D:G.48, D:L.49, D:L.49, D:V.171, D:V.171, D:G.201, D:V.359, D:T.360, D:T.360 Water bridges: D:G.10, D:G.10, D:P.39, D:G.40, D:G.40, D:F.202, D:F.202, D:V.357 pi-Stacking: D:W.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tralau, T. et al., An internal reaction chamber in dimethylglycine oxidase provides efficient protection from exposure to toxic formaldehyde. J.Biol.Chem. (2009)

Release Date

2009-04-14

Peptides

N,N-dimethylglycine oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

N,N-dimethylglycine oxidase