SMTL ID : 5nqd.2 (1 other biounit)

Arsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: 32 residues within 4Å: Chain A: G.173, H.198, N.199, K.412, W.416, H.450, G.485, C.486, D.487, T.491, V.542, D.543, I.544, I.545, T.547, A.559, A.560, T.561, D.592, N.717, R.719, Q.725, S.726, Y.728, F.791, Q.798, T.802, Y.814, K.815 Ligands: MGD.2, O.3, 4MO.4 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.173, A:D.487, A:T.491, A:T.491, A:V.542, A:I.544, A:T.561, A:N.717, A:N.717, A:R.719, A:R.719, A:Q.725, A:S.726, A:S.726, A:K.815 Water bridges: A:N.178, A:D.487, A:T.491, A:T.491 Salt bridges: A:D.543, A:D.592 pi-Stacking: A:Y.814 pi-Cation interactions: A:Y.814 MGD.2: 36 residues within 4Å: Chain A: C.26, R.103, G.235, T.236, N.237, E.240, T.241, Q.242, V.279, D.280, P.281, R.282, T.284, I.304, S.306, G.307, D.309, E.411, K.412, G.413, G.448, G.449, H.450, N.716, G.718, R.719, A.720, N.721, V.723, W.724, Q.725, K.815, Q.816 Ligands: MGD.1, O.3, 4MO.4 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.235, A:N.237, A:E.240, A:T.241, A:T.241, A:T.241, A:Q.242, A:V.279, A:R.282, A:R.282, A:G.307, A:K.412, A:G.413, A:N.716, A:R.719, A:R.719, A:V.723, A:Q.725, A:Q.725, A:Q.816 Water bridges: A:D.309, A:A.720 Salt bridges: A:D.280, A:D.309, A:R.719, A:K.815 MGD.14: 32 residues within 4Å: Chain C: G.173, H.198, N.199, K.412, W.416, H.450, G.485, C.486, D.487, T.491, V.542, D.543, I.544, I.545, T.547, A.559, A.560, T.561, D.592, N.717, R.719, Q.725, S.726, Y.728, F.791, Q.798, T.802, Y.814, K.815 Ligands: MGD.15, O.16, 4MO.17 24 PLIP interactions: 24 interactions with chain C Hydrogen bonds: C:G.173, C:G.485, C:D.487, C:T.491, C:T.491, C:T.491, C:V.542, C:I.544, C:T.561, C:N.717, C:N.717, C:R.719, C:R.719, C:Q.725, C:S.726, C:K.815 Water bridges: C:N.178, C:N.178, C:H.488, C:S.726 Salt bridges: C:D.543, C:D.592 pi-Stacking: C:Y.814 pi-Cation interactions: C:Y.814 MGD.15: 36 residues within 4Å: Chain C: R.103, V.234, G.235, T.236, N.237, E.240, T.241, Q.242, V.279, D.280, P.281, R.282, T.284, I.304, S.306, G.307, D.309, E.411, K.412, G.413, G.448, G.449, H.450, N.716, G.718, R.719, A.720, N.721, V.723, W.724, Q.725, K.815, Q.816 Ligands: MGD.14, O.16, 4MO.17 25 PLIP interactions: 25 interactions with chain C Hydrogen bonds: C:G.235, C:T.236, C:N.237, C:E.240, C:T.241, C:T.241, C:Q.242, C:V.279, C:R.282, C:R.282, C:G.307, C:K.412, C:G.413, C:N.716, C:R.719, C:R.719, C:V.723, C:Q.725, C:Q.725, C:Q.816 Water bridges: C:D.309, C:A.720 Salt bridges: C:D.309, C:R.719, C:K.815

2 x O: OXYGEN ATOM(Non-covalent)

O.3: 6 residues within 4Å: Chain A: N.199, E.206, K.412 Ligands: MGD.1, MGD.2, 4MO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.199, A:K.412, A:K.412 Water bridges: A:R.446 O.16: 6 residues within 4Å: Chain C: N.199, E.206, K.412 Ligands: MGD.14, MGD.15, 4MO.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.199, C:K.412

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

4MO.4: 6 residues within 4Å: Chain A: N.199, K.412, R.719 Ligands: MGD.1, MGD.2, O.3 No protein-ligand interaction detected (PLIP) 4MO.17: 5 residues within 4Å: Chain C: K.412, R.719 Ligands: MGD.14, MGD.15, O.16 No protein-ligand interaction detected (PLIP)

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

F3S.5: 11 residues within 4Å: Chain A: C.23, F.25, C.26, G.29, C.30, Y.32, S.101, R.103, G.104, T.243, N.244 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.23, A:C.26, A:C.30 F3S.18: 11 residues within 4Å: Chain C: C.23, F.25, C.26, V.28, G.29, C.30, Y.32, S.101, R.103, G.104, N.244 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.23, C:C.26, C:C.30

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

SO4.6: 5 residues within 4Å: Chain A: S.138, W.139, D.140 Chain C: P.828, R.829 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:W.139, A:D.140, A:D.140, C:R.829 SO4.7: 4 residues within 4Å: Chain A: R.403, R.405, R.439, P.440 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.403 Salt bridges: A:R.405 SO4.8: 3 residues within 4Å: Chain A: R.275, K.389, W.393 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.392 Salt bridges: A:R.275, A:K.389 SO4.9: 4 residues within 4Å: Chain A: E.272, K.398, E.399, R.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.399 Salt bridges: A:R.404 SO4.19: 5 residues within 4Å: Chain A: P.828, R.829 Chain C: S.138, W.139, D.140 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.829, C:W.139, C:D.140 Salt bridges: A:R.829 SO4.20: 4 residues within 4Å: Chain C: R.275, K.389, E.392, W.393 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.275, C:K.389

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

PEG.10: 6 residues within 4Å: Chain A: D.168, R.200, N.204, R.211, Y.454, D.459 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.200, A:R.211, A:D.459

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain A: L.699, A.701, G.703, K.704, Q.705, Q.706 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.703, A:K.704, A:Q.705, A:Q.706 GOL.23: 7 residues within 4Å: Chain A: N.117 Chain C: F.2, R.4, E.109, N.733, D.734, F.735 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:R.4, C:D.734, C:F.735, A:N.117, A:N.117 Water bridges: C:E.732, C:N.733 GOL.24: 8 residues within 4Å: Chain C: L.699, A.701, P.702, G.703, K.704, Q.705, Q.706 Ligands: EDO.25 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.699, C:G.703, C:K.704, C:Q.705, C:Q.706

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

EDO.12: 5 residues within 4Å: Chain A: G.672, T.673, Q.674, R.675, T.678 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.674, A:R.675, A:R.675 EDO.25: 1 residues within 4Å: Ligands: GOL.24 No protein-ligand interaction detected (PLIP)

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

FES.13: 8 residues within 4Å: Chain B: C.60, H.62, K.63, G.64, A.65, C.78, H.81, S.83 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.60, B:H.62, B:C.78, B:H.81 FES.26: 8 residues within 4Å: Chain D: C.60, H.62, K.63, A.65, C.78, H.81, F.82, S.83 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.60, D:H.62, D:C.78, D:H.81

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

P33.21: 12 residues within 4Å: Chain C: Y.176, N.204, S.205, R.211, E.217, E.452, Y.454, D.459, M.570, N.638, A.639, E.660 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Y.176, C:R.211, C:R.211, C:D.459, C:D.459, C:H.640 Water bridges: C:L.218, C:H.640, C:H.640 P33.22: 9 residues within 4Å: Chain A: H.5, Y.73, A.115, R.116 Chain C: H.5, P.10, Y.73, A.115, R.116 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Santos-Silva, T. et al., Arsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A. To Be Published

Release Date

2018-05-30

Peptides

AroA: AC
Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
G

B
D

D
H

AroA

Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster

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