SMTL ID : 8cgs.1 (1 other biounit)

Crystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to antimony oxyanion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 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: 34 residues within 4Å: Chain A: G.167, H.192, N.193, K.382, W.386, H.420, W.452, G.453, C.454, N.455, N.456, T.459, I.510, N.511, L.512, T.515, A.527, A.528, H.529, D.560, N.697, R.699, Q.705, T.706, Y.708, F.771, Q.778, T.782, Y.794, K.795 Ligands: MGD.2, O.3, 4MO.4, UJI.10 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.167, A:N.455, A:N.455, A:T.459, A:I.510, A:N.511, A:L.512, A:N.697, A:R.699, A:R.699, A:Q.705, A:T.706, A:Q.778, A:K.795 Water bridges: A:N.172, A:T.459, A:T.706, A:Y.708, A:Y.708 Salt bridges: A:D.560 MGD.2: 36 residues within 4Å: Chain A: C.21, R.98, G.229, N.230, N.231, E.234, S.235, Q.236, V.273, D.274, P.275, R.276, T.278, I.298, G.301, D.303, E.381, K.382, G.383, I.384, G.418, G.419, H.420, W.694, N.696, G.698, R.699, N.700, N.701, V.703, W.704, Q.705, K.795 Ligands: MGD.1, O.3, 4MO.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:G.229, A:N.230, A:N.231, A:E.234, A:S.235, A:S.235, A:S.235, A:Q.236, A:V.273, A:R.276, A:R.276, A:G.301, A:K.382, A:G.383, A:N.696, A:R.699, A:R.699, A:V.703, A:Q.705, A:Q.705 Water bridges: A:G.383, A:N.700 Salt bridges: A:D.303, A:R.699, A:K.795 MGD.19: 35 residues within 4Å: Chain C: G.167, H.192, N.193, K.382, W.386, H.420, W.452, G.453, C.454, N.455, N.456, T.459, I.510, N.511, L.512, Y.513, T.515, A.527, A.528, H.529, D.560, N.697, R.699, Q.705, T.706, Y.708, F.771, Q.778, T.782, Y.794, K.795 Ligands: MGD.20, O.21, 4MO.22, UJI.27 22 PLIP interactions: 22 interactions with chain C Hydrogen bonds: C:G.167, C:N.455, C:N.455, C:T.459, C:T.459, C:I.510, C:N.511, C:L.512, C:N.697, C:R.699, C:R.699, C:Q.705, C:T.706, C:T.706, C:Q.778, C:K.795 Water bridges: C:N.172, C:N.172, C:Y.708, C:Y.708, C:Y.708 Salt bridges: C:D.560 MGD.20: 38 residues within 4Å: Chain C: C.21, R.98, G.229, N.230, N.231, E.234, S.235, Q.236, V.273, D.274, P.275, R.276, T.278, I.298, P.300, G.301, D.303, E.381, K.382, G.383, I.384, G.418, G.419, H.420, W.694, N.696, G.698, R.699, N.700, N.701, V.703, W.704, Q.705, K.795 Ligands: MGD.19, O.21, 4MO.22, UJI.27 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:R.98, C:G.229, C:N.231, C:E.234, C:S.235, C:S.235, C:S.235, C:Q.236, C:V.273, C:R.276, C:R.276, C:G.301, C:K.382, C:G.383, C:N.696, C:R.699, C:R.699, C:V.703, C:Q.705, C:Q.705 Water bridges: C:D.303, C:D.303, C:N.700 Salt bridges: C:D.303, C:R.699, C:K.795

2 x O: OXYGEN ATOM(Non-covalent)

O.3: 7 residues within 4Å: Chain A: N.193, E.200, K.382 Ligands: MGD.1, MGD.2, 4MO.4, UJI.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.193, A:K.382, A:R.416 O.21: 8 residues within 4Å: Chain C: N.193, E.200, K.382, R.416 Ligands: MGD.19, MGD.20, 4MO.22, UJI.27 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.193, C:E.200, C:K.382, C:R.416

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

4MO.4: 7 residues within 4Å: Chain A: N.193, K.382, R.699 Ligands: MGD.1, MGD.2, O.3, UJI.10 No protein-ligand interaction detected (PLIP) 4MO.22: 7 residues within 4Å: Chain C: N.193, K.382, R.699 Ligands: MGD.19, MGD.20, O.21, UJI.27 No protein-ligand interaction detected (PLIP)

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

F3S.5: 11 residues within 4Å: Chain A: C.18, F.20, C.21, G.24, C.25, Y.27, S.96, R.98, G.99, T.237, N.238 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.18, A:C.21, A:C.25 F3S.23: 11 residues within 4Å: Chain C: C.18, F.20, C.21, G.24, C.25, Y.27, S.96, R.98, G.99, T.237, N.238 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.18, C:C.21, C:C.25

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 8 residues within 4Å: Chain A: T.132, D.134, H.135, A.138, T.489 Chain C: V.804, G.805, S.806 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:S.806, A:T.132, A:T.132, A:T.489 Water bridges: A:D.134, A:T.489 PEG.11: 6 residues within 4Å: Chain A: E.299, R.692, W.694, G.765, Q.766, W.798 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.692, A:W.694, A:Q.766 Water bridges: A:E.299 PEG.12: 8 residues within 4Å: Chain A: V.804, G.805, S.806 Chain C: T.132, D.134, H.135, A.138, T.489 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:D.134, C:T.489, C:T.489, A:S.806, A:S.806 Water bridges: C:D.134 PEG.24: 7 residues within 4Å: Chain C: Q.115, R.116, L.117, R.121, W.128, P.514, M.524 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.115, C:R.121

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 3 residues within 4Å: Chain A: L.657, Y.658, D.664 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.664 ACT.9: 7 residues within 4Å: Chain A: D.112, Y.712, N.713, S.714, L.715 Chain C: T.110, K.114 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:T.110 Hydrogen bonds: A:D.112, A:S.714, A:L.715 Water bridges: A:N.713, A:N.713, A:N.713, A:N.713

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 3 residues within 4Å: Chain A: K.330, G.331, F.332 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.331, A:F.332 Water bridges: A:D.333 Salt bridges: A:K.330 PO4.25: 3 residues within 4Å: Chain C: K.330, G.331, F.332 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.331, C:F.332 Water bridges: C:T.329, C:K.330, C:D.333, C:D.334 Salt bridges: C:K.330 PO4.28: 3 residues within 4Å: Chain A: R.802 Chain C: T.488, T.489 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:T.489 Water bridges: C:T.488, C:T.489, C:T.489, C:E.490, A:R.802, A:R.802 Salt bridges: A:R.802

2 x UJI: tetrakis(oxidanyl)antimony(Non-covalent)

UJI.10: 13 residues within 4Å: Chain A: H.163, H.192, N.193, E.200, R.416, G.418, G.419, H.420, Q.421, E.422 Ligands: MGD.1, O.3, 4MO.4 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:H.192, A:N.193, A:E.200, A:R.416, A:R.416, A:G.419, A:H.420, A:H.420 Water bridges: A:D.162, A:R.194 Metal complexes: O.3 UJI.27: 11 residues within 4Å: Chain C: H.163, H.192, N.193, E.200, R.416, G.419, H.420 Ligands: MGD.19, MGD.20, O.21, 4MO.22 12 PLIP interactions: 11 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:N.193, C:E.200, C:K.382, C:R.416, C:R.416, C:G.419, C:H.420 Water bridges: C:R.194, C:E.200, C:H.420, C:E.422 Metal complexes: O.21

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

CL.13: 5 residues within 4Å: Chain A: T.63, P.64, A.65 Chain B: T.99, E.100 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: R.447, Q.501 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain C: T.63, P.64, A.65 Chain D: T.99, E.100 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 7 residues within 4Å: Chain A: D.151, Q.154, G.155, G.444, K.445, G.446, R.447 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.446 Water bridges: A:G.444, A:G.446 GOL.16: 3 residues within 4Å: Chain A: R.375, R.409, R.410 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.375, A:R.375, A:R.410 GOL.26: 7 residues within 4Å: Chain C: D.151, Q.154, G.155, G.444, K.445, G.446, R.447 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.154, C:G.446 Water bridges: C:G.444, C:G.446

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.17: 8 residues within 4Å: Chain A: S.806, M.807, E.808, E.809 Chain C: T.131, T.132, W.133, T.556 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:T.131, C:W.133, A:S.806, A:E.808, A:E.809 Water bridges: C:D.134, C:R.566 TRS.30: 8 residues within 4Å: Chain A: T.131, T.132, W.133, T.556 Chain C: S.806, M.807, E.808, E.809 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:S.806, C:E.808, C:E.809, A:T.131, A:W.133 Water bridges: A:D.134, A:T.556, A:R.566, A:R.566

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

FES.18: 10 residues within 4Å: Chain B: C.60, H.62, M.63, G.64, C.65, C.78, C.80, H.81, F.82, T.83 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.60, B:C.78, B:H.81 FES.31: 9 residues within 4Å: Chain D: C.60, H.62, M.63, G.64, C.65, C.78, H.81, F.82, T.83 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.60, D:C.78, D:H.81

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

Arsenite oxidase subunit AioA: AC
AioB: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Arsenite oxidase subunit AioA

AioB

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