SMTL ID : 5ul4.1

Structure of Cobalamin-dependent S-adenosylmethionine radical enzyme OxsB with aqua-cobalamin and S-adenosylmethionine bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 11 residues within 4Å: Chain A: C.313, S.316, R.317, C.318, F.320, C.321, R.323, E.363, R.399 Ligands: B12.2, SAM.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.363 Metal complexes: A:C.313, A:C.318, A:C.321, SAM.3

1 x B12: COBALAMIN(Non-covalent)

B12.2: 31 residues within 4Å: Chain A: F.131, R.135, L.138, S.139, T.142, L.143, G.182, L.183, S.184, F.187, T.214, G.216, N.217, C.237, K.239, E.240, G.241, E.242, E.308, R.311, C.321, P.322, H.325, K.326, A.361, E.363, M.578 Ligands: SF4.1, SAM.3, EDO.16, EDO.19 31 PLIP interactions: 29 interactions with chain A, 2 Ligand-Water interactions Hydrophobic interactions: A:F.131, A:L.143, A:T.214, A:K.326, A:A.361, A:E.363 Hydrogen bonds: A:R.135, A:R.135, A:F.187, A:N.217, A:N.217, A:G.241, A:E.242, A:E.308, A:P.322, A:H.325, A:E.363, A:E.363, A:E.363 Water bridges: A:N.124, A:N.124, A:N.137, A:N.137, A:S.139, A:S.139, A:N.217, A:K.326, A:K.326 Salt bridges: A:K.326 Metal complexes: H2O.5, H2O.16

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 15 residues within 4Å: Chain A: F.320, E.363, A.397, F.432, G.434, E.436, G.472, F.473, I.474, S.543, M.544, E.545 Ligands: SF4.1, B12.2, EDO.19 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.363, A:G.434, A:E.436, A:E.545, A:E.545 Water bridges: A:R.399, A:R.399, A:K.448, A:F.473, A:E.545, A:L.547 Salt bridges: A:K.448 pi-Stacking: A:F.320

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 5 residues within 4Å: Chain A: W.88, H.89, S.107, C.108 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.109

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

EDO.5: 4 residues within 4Å: Chain A: L.14, K.18, P.75, Y.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.18 Water bridges: A:P.75, A:Y.101 EDO.6: 4 residues within 4Å: Chain A: H.89, W.92, C.108 Ligands: MES.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.92 EDO.7: 4 residues within 4Å: Chain A: T.280, L.327, R.328, S.329 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.280, A:R.328, A:R.328, A:S.329 EDO.8: 4 residues within 4Å: Chain A: Y.627, M.630, E.631, R.634 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.634 Water bridges: A:R.634 EDO.9: 6 residues within 4Å: Chain A: R.430, L.469, R.470, I.536, V.537, R.634 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.430, A:L.469 Water bridges: A:V.537, A:R.634 EDO.10: 5 residues within 4Å: Chain A: I.467, N.468, L.469, L.499, I.536 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.430, A:N.468, A:L.469 Water bridges: A:T.529 EDO.11: 4 residues within 4Å: Chain A: K.284, E.285, S.334, Q.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.285, A:S.334, A:S.334, A:Q.337 EDO.12: 4 residues within 4Å: Chain A: S.538, Y.539, M.540, R.634 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.540 Water bridges: A:H.633, A:R.634 EDO.13: 2 residues within 4Å: Chain A: H.351, F.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.351 EDO.14: 6 residues within 4Å: Chain A: M.475, L.493, Y.534, M.540, L.541, H.638 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.541, A:H.638 Water bridges: A:M.475 EDO.15: 3 residues within 4Å: Chain A: K.624, K.625, S.628 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.625, A:S.628, A:S.628 EDO.16: 3 residues within 4Å: Chain A: R.135, Y.359 Ligands: B12.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.135 EDO.17: 3 residues within 4Å: Chain A: K.393, A.424, L.425 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.393, A:K.393 Water bridges: A:G.427 EDO.18: 4 residues within 4Å: Chain A: E.113, H.114, K.253, E.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.113, A:E.255 EDO.19: 3 residues within 4Å: Chain A: Y.539 Ligands: B12.2, SAM.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.545, A:E.545

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bridwell-Rabb, J. et al., A B12-dependent radical SAM enzyme involved in oxetanocin A biosynthesis. Nature (2017)

Release Date

2017-04-19

Peptides

OxsB protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

OxsB protein

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