SMTL ID : 6bpx.1

Crystal structure of cysteine-bound ferrous form of the matured Cl2-Tyr157 human cysteine dioxygenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

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

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

1 x CYS: CYSTEINE(Non-covalent)

CYS.2: 10 residues within 4Å: Chain A: Y.58, R.60, L.75, H.86, H.88, H.140, V.142, H.155, X.157 Ligands: FE2.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.58 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: 2 residues within 4Å: Chain A: H.173, K.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.174 Water bridges: 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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: A.166, F.167, D.168, H.173, N.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.166, A:D.168 GOL.7: 3 residues within 4Å: Chain A: Y.58, S.83, S.84 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.58, A:S.84, A:S.84 Water bridges: A:Y.58, A:Y.58, A:Y.58, A:G.82, A:G.82, A:H.86 GOL.8: 3 residues within 4Å: Chain A: N.90, H.92, N.134 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.92, A:N.134 GOL.9: 6 residues within 4Å: Chain A: F.53, D.54, Q.55, G.78, E.79, H.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.55, A:E.79 Water bridges: A:F.53, A:Q.55 GOL.10: 5 residues within 4Å: Chain A: S.42, P.44, L.98, Q.99, E.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.99, A:E.127 Water bridges: A:N.128 GOL.11: 5 residues within 4Å: Chain A: R.57, H.182, R.188, P.190, N.191 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.57, A:R.57, A:H.182, A:R.188, A:R.188, A:P.190 Water bridges: A:T.180, A:H.182

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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