SMTL ID : 6bgf.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x CYS: CYSTEINE(Non-covalent)

CYS.1: 10 residues within 4Å: Chain A: Y.58, R.60, L.75, H.86, H.88, H.140, V.142, H.155, Y.157 Ligands: FE2.2 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:Y.58, A:Y.157, A:Y.157, C.1 Water bridges: A:H.155 Salt bridges: A:R.60

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

FE2.2: 4 residues within 4Å: Chain A: H.86, H.88, H.140 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.34, A:Q.34, A:Y.132 Water bridges: A:R.123 Salt bridges: A:R.123 SO4.4: 2 residues within 4Å: Chain A: H.173, K.174 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.174 Water bridges: A:K.112, A:H.173 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:R.141 Salt bridges: A:K.119, A:R.141

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: H.165, K.174, K.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.165, A:K.176 Water bridges: A:K.176 GOL.7: 5 residues within 4Å: Chain A: Y.58, S.83, S.84, C.164 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.84 Water bridges: A:G.82 GOL.8: 6 residues within 4Å: Chain A: F.53, D.54, Q.55, G.78, E.79, H.81 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.54, A:D.54, A:E.79, A:E.79 Water bridges: A:H.81 GOL.9: 4 residues within 4Å: Chain A: K.52, G.186, I.187, R.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.52, A:G.186 GOL.10: 5 residues within 4Å: Chain A: R.57, Y.58, R.60, T.180 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.180

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

2017-12-13

Peptides

Cysteine dioxygenase type 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cysteine dioxygenase type 1

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