SMTL ID : 8ch9.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 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: 36 residues within 4Å: Chain A: C.22, R.99, G.230, N.231, N.232, E.235, S.236, Q.237, V.274, D.275, P.276, R.277, T.279, I.299, G.302, D.304, E.382, K.383, G.384, I.385, G.419, G.420, H.421, W.695, N.697, G.699, R.700, N.701, N.702, V.704, W.705, Q.706, K.796 Ligands: MGD.2, ART.4, 4MO.9 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:N.231, A:N.232, A:E.235, A:S.236, A:S.236, A:S.236, A:Q.237, A:V.274, A:R.277, A:R.277, A:G.302, A:K.383, A:N.697, A:R.700, A:R.700, A:V.704, A:Q.706, A:Q.706 Water bridges: A:D.304, A:D.304, A:N.701, A:Y.794 Salt bridges: A:D.275, A:D.304, A:R.700, A:K.796 MGD.2: 34 residues within 4Å: Chain A: G.168, H.193, N.194, K.383, W.387, H.421, W.453, G.454, C.455, N.456, N.457, T.460, I.511, N.512, L.513, Y.514, T.516, A.528, A.529, H.530, D.561, N.698, R.700, Q.706, T.707, Y.709, F.772, Q.779, T.783, Y.795, K.796 Ligands: MGD.1, ART.4, 4MO.9 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.168, A:N.456, A:N.456, A:N.457, A:T.460, A:T.460, A:I.511, A:N.512, A:L.513, A:N.698, A:N.698, A:R.700, A:R.700, A:Q.706, A:T.707, A:T.707, A:K.796 Water bridges: A:N.173, A:N.173, A:T.707 Salt bridges: A:D.561 MGD.16: 36 residues within 4Å: Chain C: C.22, R.99, G.230, N.231, N.232, E.235, S.236, Q.237, V.274, D.275, P.276, R.277, T.279, I.299, G.302, D.304, E.382, K.383, G.384, I.385, G.419, G.420, H.421, W.695, N.697, G.699, R.700, N.701, N.702, V.704, W.705, Q.706, K.796 Ligands: MGD.17, ART.19, 4MO.21 26 PLIP interactions: 26 interactions with chain C Hydrogen bonds: C:G.230, C:N.231, C:N.232, C:E.235, C:S.236, C:S.236, C:S.236, C:Q.237, C:V.274, C:R.277, C:R.277, C:G.302, C:K.383, C:N.697, C:R.700, C:R.700, C:V.704, C:Q.706, C:Q.706 Water bridges: C:G.384, C:N.701, C:Y.794 Salt bridges: C:D.275, C:D.304, C:R.700, C:K.796 MGD.17: 34 residues within 4Å: Chain C: G.168, H.193, N.194, K.383, W.387, H.421, W.453, G.454, C.455, N.456, N.457, T.460, I.511, N.512, L.513, Y.514, T.516, A.528, A.529, H.530, D.561, N.698, R.700, Q.706, T.707, Y.709, F.772, Q.779, T.783, Y.795, K.796 Ligands: MGD.16, ART.19, 4MO.21 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:G.168, C:N.456, C:N.456, C:N.457, C:T.460, C:I.511, C:N.512, C:L.513, C:N.698, C:N.698, C:R.700, C:R.700, C:Q.706, C:T.707, C:K.796 Water bridges: C:N.173, C:T.460, C:T.707, C:Y.795 Salt bridges: C:D.561

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

F3S.3: 11 residues within 4Å: Chain A: C.19, F.21, C.22, G.25, C.26, Y.28, S.97, R.99, G.100, T.238, N.239 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.19, A:C.22, A:C.26 F3S.18: 11 residues within 4Å: Chain C: C.19, F.21, C.22, G.25, C.26, Y.28, S.97, R.99, G.100, T.238, N.239 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.19, C:C.22, C:C.26

2 x ART: ARSENATE(Non-covalent)

ART.4: 11 residues within 4Å: Chain A: H.193, N.194, E.201, K.383, R.417, G.420, H.421 Ligands: MGD.1, MGD.2, GOL.6, 4MO.9 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:H.193, A:N.194, A:K.383, A:R.417, A:R.417, A:G.420, A:H.421, A:H.421 Water bridges: A:E.423 ART.19: 12 residues within 4Å: Chain C: D.163, H.193, N.194, E.201, K.383, R.417, G.420, H.421 Ligands: MGD.16, MGD.17, 4MO.21, GOL.22 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:H.193, C:N.194, C:K.383, C:R.417, C:R.417, C:G.420, C:H.421, C:H.421

2 x FC6: HEXACYANOFERRATE(3-)(Non-covalent)

FC6.5: 6 residues within 4Å: Chain A: D.737, T.739, D.742, K.804, S.807, K.812 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.804, A:S.807, A:K.812 FC6.20: 6 residues within 4Å: Chain C: D.737, T.739, D.742, K.804, S.807, K.812 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.804, C:S.807, C:K.812

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: D.163, H.193, R.195, E.201, R.417, E.423, Q.618 Ligands: ART.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.163, A:R.195, A:R.195, A:E.201, A:R.417, A:Q.618 GOL.7: 5 residues within 4Å: Chain A: K.87, A.88, C.89, V.90, S.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.87 Water bridges: A:V.90, A:S.93 GOL.8: 7 residues within 4Å: Chain A: H.29, D.86, A.88, S.634, G.635, N.636, N.637 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.636, A:N.636, A:N.637 Water bridges: A:N.16 GOL.22: 8 residues within 4Å: Chain C: D.163, H.193, R.195, E.201, R.417, E.423, Q.618 Ligands: ART.19 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.195, C:R.195, C:E.201, C:R.417, C:Q.618 Water bridges: C:R.206, C:R.206, C:E.423 GOL.23: 5 residues within 4Å: Chain C: K.87, A.88, C.89, V.90, S.93 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.90, C:S.93 GOL.24: 3 residues within 4Å: Chain C: D.292, R.360, W.364 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.292, C:W.364 Water bridges: C:R.270, C:R.270, C:R.270, C:D.292 GOL.25: 8 residues within 4Å: Chain C: D.163, I.192, R.195, Y.198, N.199, S.200, R.206, Y.425 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.163, C:D.163, C:R.195, C:R.206 Water bridges: C:Y.198, C:S.200, C:R.206, C:R.206

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

4MO.9: 4 residues within 4Å: Chain A: R.700 Ligands: MGD.1, MGD.2, ART.4 No protein-ligand interaction detected (PLIP) 4MO.21: 4 residues within 4Å: Chain C: R.700 Ligands: MGD.16, MGD.17, ART.19 No protein-ligand interaction detected (PLIP)

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

EDO.10: 6 residues within 4Å: Chain A: D.163, R.195, N.199, S.200, Y.425 Ligands: PEG.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.163, A:R.195 EDO.12: 4 residues within 4Å: Chain A: N.2, R.4, T.6 Chain D: T.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.2, D:T.3, D:T.3 Water bridges: A:N.2, A:T.6 EDO.13: 7 residues within 4Å: Chain A: Q.55, L.56, P.57, P.58 Chain B: L.60, G.65, Y.127 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.65 Water bridges: A:L.56 EDO.15: 4 residues within 4Å: Chain A: Q.250 Chain B: P.80, C.81, F.83 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.81, A:Q.250 EDO.26: 3 residues within 4Å: Chain C: E.809, K.812, R.813 No protein-ligand interaction detected (PLIP)

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

PEG.11: 5 residues within 4Å: Chain A: Y.198, P.429, Y.430, D.616 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.198, A:Y.430, A:D.616

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

FES.14: 10 residues within 4Å: Chain B: C.61, H.63, M.64, G.65, C.66, C.79, C.81, H.82, F.83, T.84 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.61, B:H.63, B:C.79, B:H.82 FES.27: 10 residues within 4Å: Chain D: C.61, H.63, M.64, G.65, C.66, C.79, C.81, H.82, F.83, T.84 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.61, D:H.63, D:C.79, D:H.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Engrola, F. et al., Crystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to arsenic oxyanion. To Be Published

Release Date

2024-02-21

Peptides

Arsenite oxidase subunit AioA: AC
Arsenite oxidase subunit AioB: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
E

B
D

D
F

Arsenite oxidase subunit AioA

Arsenite oxidase subunit AioB

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