SMTL ID : 6bps.1

Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 human cysteine dioxygenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: H.86, H.88, H.140 Ligands: CYS.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.86, A:H.88, A:H.140, CYS.2, H2O.4

1 x CYS: CYSTEINE(Non-covalent)

CYS.2: 12 residues within 4Å: Chain A: Y.58, R.60, L.75, H.86, H.88, H.140, V.142, H.155, X.157, M.179 Ligands: FE2.1, GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.58 Water bridges: A:H.155 Salt bridges: A:R.60

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

SO4.3: 4 residues within 4Å: Chain A: Q.34, R.123, A.131, Y.132 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.34, A:Y.132, A:Y.132 Water bridges: A:R.123 Salt bridges: A:R.123 SO4.4: 3 residues within 4Å: Chain A: G.172, H.173, K.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.174 Salt bridges: A:H.173, A:K.174 SO4.5: 3 residues within 4Å: Chain A: K.119, R.141, Q.169 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.169 Water bridges: A:K.119, A:K.119 Salt bridges: A:K.119, A:R.141

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: Y.58, S.83, S.84, H.86, C.164 Ligands: CYS.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:Y.58, A:S.84, C.2 Water bridges: A:G.82 GOL.7: 2 residues within 4Å: Chain A: W.109, D.135 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.135 GOL.8: 3 residues within 4Å: Chain A: N.90, H.92, N.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.92, A:N.134 Water bridges: A:D.135 GOL.9: 6 residues within 4Å: Chain A: A.166, F.167, D.168, H.173, K.174, N.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.168, A:H.173, A:N.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Cleavage of a carbon-fluorine bond by an engineered cysteine dioxygenase. Nat. Chem. Biol. (2018)

Release Date

2018-07-04

Peptides

Cysteine dioxygenase type 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cysteine dioxygenase type 1

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