SMTL ID : 6cdn.1

Crystal structure of cysteine-bound ferrous form of the crosslinked Cl-Tyr157 human cysteine dioxygenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x CYS: CYSTEINE(Non-covalent)

CYS.1: 11 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: FE2.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:Y.58, C.1, C.1 Water bridges: A:H.155 Salt bridges: A:R.60

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

FE2.2: 5 residues within 4Å: Chain A: H.86, H.88, H.140, X.157 Ligands: CYS.1 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.1, H2O.1

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

SO4.3: 4 residues within 4Å: Chain A: Q.34, R.123, A.131, Y.132 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.34, A:Q.34, A:Y.132 Water bridges: A:R.123, A:R.123 Salt bridges: A:R.123 SO4.4: 2 residues within 4Å: Chain A: H.173, K.174 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.174 Water bridges: A:K.112, A:G.172, A:G.172, 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.169 Water bridges: A:K.103, A:K.119, A:R.141 Salt bridges: A:K.119, A:R.141

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: F.53, D.54, Q.55, G.78, E.79, H.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.79, A:E.79 GOL.7: 2 residues within 4Å: Chain A: L.98, E.127 5 PLIP interactions: 5 interactions with chain A Water bridges: A:L.98, A:G.100, A:G.100, A:N.101, A:E.127

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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