SMTL ID : 8ccq.2 (1 other biounit)

Crystal structure of arsenite oxidase from Pseudorhizobium banfieldiae str. NT-26 (NT-26 Aio) bound to antimony trioxide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-2-2-mer

Ligands

4 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.1: 33 residues within 4Å: Chain A: G.174, H.199, N.200, K.413, W.417, H.451, G.486, C.487, D.488, T.492, V.543, D.544, I.545, I.546, T.548, A.560, A.561, T.562, D.593, N.718, R.720, Q.726, S.727, Y.729, F.792, Q.799, T.803, Y.815, K.816 Ligands: MGD.2, O.3, O.4, 4MO.5 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.174, A:D.488, A:D.488, A:T.492, A:V.543, A:I.545, A:T.562, A:N.718, A:N.718, A:R.720, A:R.720, A:Q.726, A:S.727, A:S.727, A:K.816 Water bridges: A:G.175, A:T.492, A:T.492 Salt bridges: A:D.544, A:D.593 pi-Stacking: A:Y.815 pi-Cation interactions: A:Y.815 MGD.2: 36 residues within 4Å: Chain A: R.104, G.236, T.237, N.238, E.241, T.242, Q.243, V.280, D.281, P.282, R.283, T.285, I.305, S.307, G.308, D.310, E.412, K.413, G.414, G.449, G.450, H.451, N.717, G.719, R.720, A.721, N.722, V.724, W.725, Q.726, K.816, Q.817 Ligands: MGD.1, O.3, O.4, 4MO.5 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.236, A:N.238, A:E.241, A:T.242, A:T.242, A:T.242, A:Q.243, A:V.280, A:R.283, A:R.283, A:G.308, A:K.413, A:G.414, A:N.717, A:R.720, A:R.720, A:V.724, A:Q.726, A:Q.726, A:Q.817 Water bridges: A:D.310, A:A.721 Salt bridges: A:D.310, A:R.720, A:K.816 MGD.14: 33 residues within 4Å: Chain C: G.174, H.199, N.200, K.413, W.417, H.451, G.486, C.487, D.488, T.492, V.543, D.544, I.545, I.546, T.548, A.560, A.561, T.562, D.593, N.718, R.720, Q.726, S.727, Y.729, F.792, Q.799, T.803, Y.815, K.816 Ligands: MGD.15, O.16, O.17, 4MO.18 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:G.174, C:D.488, C:T.492, C:T.492, C:T.492, C:V.543, C:I.545, C:T.562, C:N.718, C:N.718, C:R.720, C:R.720, C:Q.726, C:S.727, C:S.727, C:K.816 Water bridges: C:G.175, C:N.179 Salt bridges: C:D.544, C:D.593 pi-Stacking: C:Y.815 pi-Cation interactions: C:Y.815 MGD.15: 38 residues within 4Å: Chain C: R.104, V.235, G.236, T.237, N.238, E.241, T.242, Q.243, V.280, D.281, P.282, R.283, T.285, I.305, S.307, G.308, D.310, E.412, K.413, G.414, G.449, G.450, H.451, N.717, G.719, R.720, A.721, N.722, V.724, W.725, Q.726, K.816, Q.817 Ligands: MGD.14, O.16, O.17, 4MO.18, SBO.26 27 PLIP interactions: 27 interactions with chain C Hydrogen bonds: C:T.237, C:N.238, C:E.241, C:T.242, C:T.242, C:Q.243, C:V.280, C:R.283, C:R.283, C:G.308, C:K.413, C:G.414, C:N.717, C:R.720, C:R.720, C:V.724, C:Q.726, C:Q.726, C:Q.817 Water bridges: C:R.104, C:T.285, C:D.310, C:A.721 Salt bridges: C:D.281, C:D.310, C:R.720, C:K.816

4 x O: OXYGEN ATOM(Non-covalent)

O.3: 9 residues within 4Å: Chain A: N.200, E.207, K.413, R.447 Ligands: MGD.1, MGD.2, O.4, 4MO.5, SBO.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.200, A:K.413, A:K.413, A:R.447 O.4: 7 residues within 4Å: Chain A: H.199, H.451 Ligands: MGD.1, MGD.2, O.3, 4MO.5, SBO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.451 O.16: 9 residues within 4Å: Chain C: N.200, E.207, K.413, R.447 Ligands: MGD.14, MGD.15, O.17, 4MO.18, SBO.26 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.200, C:E.207, C:K.413, C:R.447 O.17: 7 residues within 4Å: Chain C: H.199, H.451 Ligands: MGD.14, MGD.15, O.16, 4MO.18, SBO.26 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.451, C:H.451

2 x 4MO: MOLYBDENUM(IV) ION(Non-covalent)

4MO.5: 7 residues within 4Å: Chain A: K.413, R.720 Ligands: MGD.1, MGD.2, O.3, O.4, SBO.11 No protein-ligand interaction detected (PLIP) 4MO.18: 6 residues within 4Å: Chain C: R.720 Ligands: MGD.14, MGD.15, O.16, O.17, SBO.26 No protein-ligand interaction detected (PLIP)

2 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.6: 11 residues within 4Å: Chain A: C.24, F.26, C.27, G.30, C.31, Y.33, S.102, R.104, G.105, T.244, N.245 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.24, A:C.27, A:C.31 F3S.19: 11 residues within 4Å: Chain C: C.24, F.26, C.27, G.30, C.31, Y.33, S.102, R.104, G.105, T.244, N.245 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.24, C:C.27, C:C.31

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

SO4.7: 5 residues within 4Å: Chain A: S.139, W.140, D.141 Chain C: P.829, R.830 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:W.140, A:D.141, A:D.141, C:R.830 Water bridges: A:D.141 SO4.8: 4 residues within 4Å: Chain A: R.404, R.406, R.440, P.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.404 Salt bridges: A:R.406 SO4.9: 4 residues within 4Å: Chain A: R.276, K.390, E.393, W.394 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.393 Water bridges: A:K.390, A:W.394 Salt bridges: A:R.276, A:K.390 SO4.20: 5 residues within 4Å: Chain A: P.829, R.830 Chain C: S.139, W.140, D.141 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:W.140, C:D.141, A:R.830 Water bridges: C:S.139, C:S.139, A:R.830, A:R.830, A:N.831 Salt bridges: A:R.830 SO4.21: 3 residues within 4Å: Chain C: R.276, K.390, W.394 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.276, C:K.390

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 8 residues within 4Å: Chain A: F.3, R.5, E.110, E.733, N.734, D.735, F.736 Chain C: N.118 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:N.118, A:R.5, A:E.733, A:D.735, A:F.736 Water bridges: A:D.735 GOL.24: 8 residues within 4Å: Chain A: N.118 Chain C: F.3, R.5, E.110, E.733, N.734, D.735, F.736 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.5, C:E.110, C:E.733, C:D.735, C:F.736, A:N.118, A:N.118 GOL.25: 7 residues within 4Å: Chain C: L.700, A.702, P.703, G.704, K.705, Q.706, Q.707 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.700, C:G.704, C:K.705, C:Q.706, C:Q.707 Water bridges: C:Q.707

2 x SBO: TRIHYDROXYANTIMONITE(III)(Non-covalent)

SBO.11: 11 residues within 4Å: Chain A: H.170, H.199, N.200, E.207, K.413, R.447, G.450, H.451 Ligands: O.3, O.4, 4MO.5 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:H.199, A:K.413, A:R.447, A:R.447, A:H.451 Water bridges: A:R.201, A:E.207, A:G.450, A:G.450 Metal complexes: O.3, O.4 SBO.26: 12 residues within 4Å: Chain C: H.170, H.199, N.200, E.207, K.413, R.447, G.450, H.451 Ligands: MGD.15, O.16, O.17, 4MO.18 12 PLIP interactions: 10 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:H.199, C:E.207, C:K.413, C:R.447, C:R.447, C:H.451, C:H.451 Water bridges: C:R.201, C:G.450, C:G.450 Metal complexes: O.16, O.17

3 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.12: 12 residues within 4Å: Chain A: D.169, Y.177, N.205, S.206, R.212, E.218, E.453, Y.455, D.460, M.571, A.640, E.661 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.177, A:R.201, A:R.212 Water bridges: A:E.218, A:L.219, A:H.641, A:E.661 P33.22: 12 residues within 4Å: Chain C: Y.177, N.205, S.206, R.212, E.218, E.453, Y.455, D.460, M.571, N.639, A.640, E.661 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.177, C:R.212, C:R.212, C:D.460, C:H.641 Water bridges: C:H.641, C:H.641 P33.23: 14 residues within 4Å: Chain A: H.6, I.7, P.11, Y.74, A.116, R.117 Chain C: R.5, H.6, I.7, P.11, Y.74, V.76, A.116, R.117 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.74, A:R.117 Water bridges: C:R.117, C:R.117

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.13: 9 residues within 4Å: Chain B: C.103, H.105, K.106, G.107, F.108, C.121, H.124, F.125, S.126 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.103, B:H.105, B:C.121, B:H.124 FES.27: 9 residues within 4Å: Chain D: C.103, H.105, K.106, G.107, F.108, C.121, H.124, F.125, S.126 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.103, D:H.105, D:C.121, D:H.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Engrola, F. et al., Arsenite oxidase in complex with antimonite and arsenite oxyanions: Insights into the catalytic mechanism. J.Biol.Chem. (2023)

Release Date

2023-07-12

Peptides

AroA: AC
AroB: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
G

B
D

D
H

AroA

AroB

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