SMTL ID : 5k8z.1 (1 other biounit)

Crystal structure of dimeric chlorite dismutase from Cyanothece sp. PCC7425 (pH 8.5)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.1: 9 residues within 4Å: Chain A: Y.11, F.13, I.42, L.83, N.84, R.134, L.136, W.150, E.152 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.11, A:W.150 Hydrogen bonds: A:R.134 Water bridges: A:W.150

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.2: 32 residues within 4Å: Chain A: I.65, R.66, Y.67, A.68, L.76, I.94, I.96, K.98, W.102, F.114, H.120, T.121, G.124, L.125, Y.127, L.128, V.131, R.133, L.135, H.137, F.147, T.149, F.151, F.161, L.164, L.165, M.168, R.169, E.173, W.174, E.180 Ligands: OH.3 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.76, A:L.76, A:I.94, A:F.114, A:L.128, A:V.131, A:L.135, A:L.135, A:F.147, A:F.147, A:F.151, A:F.151, A:L.164, A:W.174 Hydrogen bonds: A:R.66, A:Y.67, A:A.68, A:W.102 Water bridges: A:Y.67, A:Y.67 Salt bridges: A:K.98 Metal complexes: A:H.120, OH.3 HEM.5: 32 residues within 4Å: Chain B: I.65, R.66, Y.67, A.68, L.76, I.94, I.96, K.98, W.102, F.114, H.120, T.121, G.124, L.125, Y.127, L.128, V.131, R.133, L.135, H.137, F.147, T.149, F.151, F.161, L.164, L.165, M.168, R.169, E.173, W.174, E.180 Ligands: OH.6 23 PLIP interactions: 22 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.76, B:L.76, B:F.114, B:V.131, B:L.135, B:L.135, B:F.147, B:F.147, B:T.149, B:F.151, B:F.151, B:L.164, B:W.174, B:W.174 Hydrogen bonds: B:R.66, B:Y.67, B:A.68, B:W.102 Water bridges: B:Y.67, B:Y.67 Salt bridges: B:K.98 Metal complexes: B:H.120, OH.6

2 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 5 residues within 4Å: Chain A: R.133, L.135, T.149, F.151 Ligands: HEM.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.133 OH.6: 5 residues within 4Å: Chain B: R.133, L.135, T.149, F.151 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.133

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 9 residues within 4Å: Chain B: Y.11, F.13, W.21, I.42, L.83, N.84, R.134, L.136, W.150 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.11, B:I.42, B:I.42, B:R.134, B:L.136, B:W.150 Hydrogen bonds: B:R.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schaffner, I. et al., Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies. ACS Catal (2017)

Release Date

2017-06-21

Peptides

Chlorite dismutase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chlorite dismutase

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