SMTL ID : 5y9i.1

Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with Co(II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.127, F.150, R.162 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.70, A:N.70, A:S.125, A:R.162 Salt bridges: A:R.127, A:R.162

1 x CO: COBALT (II) ION(Non-covalent)

CO.2: 3 residues within 4Å: Chain A: H.146, D.148, H.260 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.146, A:D.148, A:H.260, H2O.2, H2O.4, H2O.10

1 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.3: 5 residues within 4Å: Chain A: A.106, H.109, L.110, P.113, G.116 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.106, A:H.109, A:L.110 Water bridges: A:S.117

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: R.174, W.176, V.262, L.268 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: P.151, S.152 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: G.199, R.201, F.202, Y.213 Ligand excluded by PLIP

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 4 residues within 4Å: Chain A: E.22, E.102, K.103, A.106 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.106 Salt bridges: A:K.103 ACT.8: 4 residues within 4Å: Chain A: R.76, A.122, R.123, H.274 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.123, A:R.123, A:R.123, A:R.123 Salt bridges: A:R.76, A:R.123, A:H.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chung, H.S. et al., Biochemical and structural insights of Fe(II)/alpha-ketoglutarate/O2-dependent dioxygenase, KdoO from Methylacidiphilum infernorum V4. To Be Published

Release Date

2018-10-31

Peptides

Uncharacterized protein KdoO: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Uncharacterized protein KdoO

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