SMTL ID : 3moo.1 (1 other biounit)

Crystal structure of the HmuO, heme oxygenase from Corynebacterium diphtheriae, in complex with azide-bound verdoheme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 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: K.13, A.17, H.20, E.21 Ligands: VEA.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.13, A:K.13, A:E.21, A:E.21

1 x AZI: AZIDE ION(Non-covalent)

AZI.2: 5 residues within 4Å: Chain A: G.135, S.138, G.139, G.140 Ligands: VEA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.139, A:G.140

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

SO4.3: 4 residues within 4Å: Chain A: E.81, A.84, R.85, R.97 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.85, A:R.97 SO4.4: 2 residues within 4Å: Chain A: Q.58, R.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.58, A:R.117 SO4.5: 4 residues within 4Å: Chain A: G.67, A.69, E.70, S.71 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.69, A:E.70, A:S.71 Water bridges: A:A.69, A:L.72 SO4.6: 2 residues within 4Å: Chain A: S.26, T.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.27, A:T.27 SO4.7: 6 residues within 4Å: Chain A: I.166, A.167, K.168, V.171, Y.172, E.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.167, A:K.168, A:Y.172, A:E.175 Salt bridges: A:K.168

1 x VEA: 5-OXA-PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

VEA.8: 20 residues within 4Å: Chain A: K.13, H.20, A.23, E.24, M.29, L.33, Y.130, V.131, R.132, L.134, G.135, S.138, G.139, K.173, R.177, F.201, N.204, F.208 Ligands: GLC-FRU.1, AZI.2 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:A.23, A:E.24, A:L.33, A:Y.130, A:V.131, A:L.134, A:F.201, A:N.204, A:F.208 Hydrogen bonds: A:S.138 Salt bridges: A:K.13, A:K.173, A:R.177 Metal complexes: A:H.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lai, W. et al., Enzymatic ring-opening mechanism of verdoheme by the heme oxygenase: a combined X-ray crystallography and QM/MM study. J.Am.Chem.Soc. (2010)

Release Date

2011-03-09

Peptides

Heme oxygenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Heme oxygenase

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