SMTL ID : 6xtl.1

Crystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:Ag:S complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x AG: SILVER ION(Non-covalent)

AG.1: 5 residues within 4Å: Chain A: W.229, C.270, C.275, R.277 Chain B: C.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:C.270, A:C.275, B:C.6

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 8 residues within 4Å: Chain A: N.223, V.224, A.225, G.226, V.228, E.230, G.265, G.266 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:V.224, A:G.226, A:V.228 CA.3: 4 residues within 4Å: Chain A: N.189, I.190, D.203, Y.205 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:I.190, A:D.203, A:Y.205, H2O.1, H2O.2

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 9 residues within 4Å: Chain A: W.176, A.215, P.216, N.217, L.221, Y.222, N.223, V.224, A.225 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.217, A:L.221, A:N.223, A:V.224, A:A.225, A:A.225 EDO.5: 5 residues within 4Å: Chain A: H.92, E.122, R.131, G.207, T.208 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.92, A:T.208, A:T.208 Water bridges: A:R.131, A:R.131, A:G.207, A:T.208

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: R.131, P.132, N.133, H.134 Ligand excluded by PLIP

1 x SOA: ISATOIC ANHYDRIDE(Covalent)

SOA.7: 4 residues within 4Å: Chain A: Y.274 Chain B: A.1, T.2, P.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.274, B:P.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leisinger, F. et al., Non-Coordinative Binding of O2 at the Active Center of a Copper-Dependent Enzyme. Angew.Chem.Int.Ed.Engl. (2020)

Release Date

2021-01-27

Peptides

Formylglycine-generating enzyme: A
Abz-ALA-THR-THR-PRO-LEU-CYS-GLY-PRO-SER-ARG-ALA-SER-ILE-LEU-SER-GLY: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Formylglycine-generating enzyme

Abz-ALA-THR-THR-PRO-LEU-CYS-GLY-PRO-SER-ARG-ALA-SER-ILE-LEU-SER-GLY

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