SMTL ID : 6g1b.1

Corynebacterium glutamicum OxyR, oxidized form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 2 residues within 4Å: Chain A: H.141 Chain B: H.141 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.141, A:H.141, H2O.3, H2O.10 NI.10: 2 residues within 4Å: Chain C: H.141 Chain D: H.141 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:H.141, C:H.141, H2O.14, H2O.22

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 2 residues within 4Å: Chain A: Q.299, L.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.299, A:Q.299 FMT.7: 6 residues within 4Å: Chain B: H.27, F.28, S.61, T.62, R.63, K.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.28, B:S.61 FMT.8: 3 residues within 4Å: Chain A: R.265 Chain B: T.264, R.265 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.264, B:T.264 Water bridges: B:R.265, A:R.265 FMT.11: 2 residues within 4Å: Chain C: Q.299, L.302 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.299, C:Q.299 FMT.16: 6 residues within 4Å: Chain D: H.27, F.28, S.61, T.62, R.63, K.64 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.28, D:S.61 FMT.17: 3 residues within 4Å: Chain C: R.265 Chain D: T.264, R.265 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:R.265, D:R.265 Hydrogen bonds: D:T.264

2 x 1PS: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE(Non-covalent)

1PS.3: 5 residues within 4Å: Chain A: K.166, S.289, S.290, S.291, S.292 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.166 1PS.12: 5 residues within 4Å: Chain C: K.166, S.289, S.290, S.291, S.292 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.166

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: P.102, E.131, H.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.131, A:E.131 NA.13: 3 residues within 4Å: Chain C: P.102, E.131, H.133 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.131

6 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.5: 3 residues within 4Å: Chain A: D.137, H.141, L.145 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.141, B:R.234 PEO.6: 5 residues within 4Å: Chain A: K.166, E.167, I.168, Y.287, E.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.167, A:Y.287 PEO.9: 3 residues within 4Å: Chain B: I.168, P.169, Q.305 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.305, B:Q.305 PEO.14: 3 residues within 4Å: Chain C: D.137, H.141, L.145 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.137, C:D.137, D:R.234 PEO.15: 5 residues within 4Å: Chain C: K.166, E.167, I.168, Y.287, E.298 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.287, C:E.298, C:E.298 PEO.18: 3 residues within 4Å: Chain D: I.168, P.169, Q.305 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.169, D:Q.305, D:Q.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedre, B. et al., Structural snapshots of OxyR reveal the peroxidatic mechanism of H2O2sensing. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-12-05

Peptides

Hydrogen peroxide-inducible genes activator: AC
Hydrogen peroxide-inducible genes activator: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

C
J

B
B

D
B

Hydrogen peroxide-inducible genes activator

Hydrogen peroxide-inducible genes activator