SMTL ID : 8ed4.1 (1 other biounit)

Structure of the complex between the arsenite oxidase and its native electron acceptor cytochrome c552 from Pseudorhizobium sp. str. NT-26

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-2-2-2-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, 4MO.3, O.5 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.173, A:W.416, A:G.485, A:D.487, A:D.487, A:T.491, A:V.542, A:V.542, A:I.544, A:T.561, A:N.717, A:R.719, A:R.719, A:Q.725, A:S.726, A:K.815 Water bridges: A:G.174, A:N.178, A:S.726, A:G.792 Salt bridges: A:D.543, A:D.592 pi-Stacking: A:Y.814 pi-Cation interactions: A:Y.814 MGD.2: 37 residues within 4Å: Chain A: C.26, 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.1, 4MO.3, O.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:G.235, A:T.236, A:N.237, A:E.240, A:T.241, A:T.241, A:T.241, A:Q.242, A:V.279, A:V.279, A:R.282, A:R.282, A:G.307, A:K.412, A:N.716, A:R.719, A:R.719, A:Q.725, A:Q.816 Water bridges: A:D.309 Salt bridges: A:D.309, A:R.719, A:K.815 MGD.8: 32 residues within 4Å: Chain D: 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.9, 4MO.10, O.12 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:G.173, D:W.416, D:D.487, D:D.487, D:T.491, D:V.542, D:V.542, D:I.544, D:T.561, D:N.717, D:R.719, D:R.719, D:Q.725, D:S.726, D:K.815 Water bridges: D:G.174, D:N.178, D:D.487, D:D.487, D:D.592, D:G.792 Salt bridges: D:D.543, D:D.592 pi-Stacking: D:Y.814 pi-Cation interactions: D:Y.814 MGD.9: 37 residues within 4Å: Chain D: C.26, 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.8, 4MO.10, O.12 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:G.235, D:T.236, D:N.237, D:E.240, D:T.241, D:T.241, D:T.241, D:Q.242, D:V.279, D:V.279, D:R.282, D:R.282, D:G.307, D:K.412, D:G.413, D:N.716, D:R.719, D:R.719, D:Q.725, D:Q.816 Water bridges: D:T.284, D:D.309, D:A.720 Salt bridges: D:D.309, D:R.719, D:K.815

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

4MO.3: 5 residues within 4Å: Chain A: K.412, R.719 Ligands: MGD.1, MGD.2, O.5 No protein-ligand interaction detected (PLIP) 4MO.10: 6 residues within 4Å: Chain D: N.199, K.412, R.719 Ligands: MGD.8, MGD.9, O.12 No protein-ligand interaction detected (PLIP)

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

F3S.4: 12 residues within 4Å: Chain A: C.23, F.25, C.26, V.28, 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.11: 12 residues within 4Å: Chain D: C.23, F.25, C.26, V.28, G.29, C.30, Y.32, S.101, R.103, G.104, T.243, N.244 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.23, D:C.26, D:C.30

2 x O: OXYGEN ATOM(Non-covalent)

O.5: 6 residues within 4Å: Chain A: N.199, E.206, K.412 Ligands: MGD.1, MGD.2, 4MO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.199, A:E.206, A:K.412 O.12: 6 residues within 4Å: Chain D: N.199, E.206, K.412 Ligands: MGD.8, MGD.9, 4MO.10 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.198, D:N.199, D:K.412 Water bridges: D:R.446

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

FES.6: 8 residues within 4Å: Chain B: C.90, H.92, K.93, G.94, F.95, C.108, H.111, S.113 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.90, B:H.92, B:C.108, B:H.111 FES.13: 8 residues within 4Å: Chain E: C.90, H.92, K.93, F.95, C.108, H.111, F.112, S.113 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.90, E:H.92, E:C.108, E:H.111

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.7: 25 residues within 4Å: Chain B: P.96 Chain C: K.15, C.16, C.19, H.20, V.30, P.32, L.34, L.37, R.40, V.42, A.43, F.48, Y.50, S.51, F.54, W.64, L.69, Y.72, L.73, T.83, K.84, M.85, F.87, L.90 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:V.30, C:P.32, C:L.34, C:L.34, C:L.37, C:F.48, C:F.54, C:W.64, C:L.69, C:L.73, C:K.84, C:F.87, C:L.90 Hydrogen bonds: C:A.43, C:S.51, C:T.83, C:K.84 Water bridges: C:R.40, C:R.40 Salt bridges: C:R.40 pi-Stacking: C:Y.72 Metal complexes: C:H.20 HEM.14: 23 residues within 4Å: Chain E: P.96 Chain F: K.15, C.16, C.19, H.20, V.30, P.32, L.34, R.40, A.43, F.48, Y.50, S.51, F.54, W.64, L.69, Y.72, L.73, T.83, K.84, M.85, F.87, L.90 20 PLIP interactions: 19 interactions with chain F, 1 interactions with chain E, Hydrophobic interactions: F:L.34, F:F.54, F:F.54, F:W.64, F:L.69, F:K.84, F:M.85, F:F.87, F:L.90, E:P.96 Hydrogen bonds: F:A.43, F:S.51, F:T.83, F:T.83, F:K.84 Water bridges: F:R.40, F:V.45 Salt bridges: F:R.40 pi-Stacking: F:Y.72 Metal complexes: F:H.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poddar, N. et al., The structure of the complex between the arsenite oxidase from Pseudorhizobium banfieldiae sp. strain NT-26 and its native electron acceptor cytochrome c 552. Acta Crystallogr D Struct Biol (2023)

Release Date

2023-04-12

Peptides

AroA: AD
AroB: BE
C-type cytochrome c552: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

E
D

C
I

F
J

AroA

AroB

C-type cytochrome c552

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