SMTL ID : 6bpr.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: H.86, H.88, H.140 Ligands: CYS.2, NO.3 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain A Metal complexes: CYS.2, NO.3, A:H.86, A:H.88, A:H.140

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: FE.1, NO.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:Y.58, C.2, C.2 Salt bridges: A:R.60

1 x NO: NITRIC OXIDE(Non-covalent)

NO.3: 7 residues within 4Å: Chain A: H.86, H.88, H.140, H.155, X.157 Ligands: FE.1, CYS.2 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrogen bonds: C.2, A:H.155

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

SO4.4: 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 SO4.5: 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 SO4.6: 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

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: A.166, F.167, D.168, H.173, K.174, N.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.175, A:N.175 GOL.8: 5 residues within 4Å: Chain A: Y.58, S.83, S.84, H.86, C.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.84, A:S.84 Water bridges: A:G.82 GOL.9: 3 residues within 4Å: Chain A: H.165, K.174, K.176 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.174, A:K.176, A:K.176 Water bridges: A:K.174, A:N.175 GOL.10: 5 residues within 4Å: Chain A: S.42, P.44, L.98, Q.99, E.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.42, A:Q.99, A:N.128 Water bridges: A:L.98, A:N.128 GOL.11: 3 residues within 4Å: Chain A: N.101, R.126, E.127 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.101, A:E.127 Water bridges: A:G.100, A:N.101 GOL.12: 3 residues within 4Å: Chain A: T.180, F.181, K.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.181, A:K.184 Water bridges: A:K.184 GOL.13: 2 residues within 4Å: Chain A: K.8, R.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.10

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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