SMTL ID : 6n42.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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, Y.157 Ligands: CYS.2 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain A Metal complexes: CYS.2, A:H.86, A:H.88, A:H.140

1 x CYS: CYSTEINE(Non-covalent)

CYS.2: 9 residues within 4Å: Chain A: Y.58, R.60, L.75, H.86, H.88, H.140, H.155, Y.157 Ligands: FE2.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.157, A:Y.157 Water bridges: A:Y.58 Salt bridges: A:R.60

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.58, S.83, S.84, V.177 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.58, A:S.84, A:S.84 Water bridges: A:Y.58, A:G.82, A:G.82, A:S.84 GOL.4: 3 residues within 4Å: Chain A: N.90, H.92, N.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.134 Water bridges: A:H.92, A:D.135 GOL.5: 3 residues within 4Å: Chain A: Q.99, G.100, E.127 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.100 Water bridges: A:L.98, A:Q.99, A:N.101, A:N.101, A:N.128 GOL.6: 4 residues within 4Å: Chain A: T.180, F.181, H.182, R.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.180, A:H.182, A:R.188 Water bridges: A:H.182 GOL.7: 6 residues within 4Å: Chain A: F.53, D.54, Q.55, G.78, E.79, H.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.55, A:E.79, A:E.79

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

SO4.8: 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 SO4.9: 3 residues within 4Å: Chain A: K.119, R.141, Q.169 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.169 Water bridges: A:K.103, A:K.103, A:R.141, A:R.141 Salt bridges: A:K.119, A:R.141 SO4.10: 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:G.172, A:K.174 Salt bridges: A:H.173, A:K.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Probing the Cys-Tyr Cofactor Biogenesis in Cysteine Dioxygenase by the Genetic Incorporation of Fluorotyrosine. Biochemistry (2019)

Release Date

2019-04-17

Peptides

Cysteine dioxygenase type 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cysteine dioxygenase type 1

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