SMTL ID : 5g5h.1

Escherichia coli Periplasmic Aldehyde Oxidase R440H mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

FES.1: 8 residues within 4Å: Chain A: Q.157, C.158, G.159, C.161, C.208, R.209, C.210 Chain C: M.190 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.158, A:C.161, A:C.208, A:C.210 FES.2: 9 residues within 4Å: Chain A: G.98, C.99, D.100, G.102, Q.103, C.104, G.105, C.107, C.119 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.99, A:C.104, A:C.107, A:C.119

8 x IOD: IODIDE ION(Non-functional Binders)

IOD.3: 5 residues within 4Å: Chain A: K.97, C.99 Chain C: P.192, R.272 Ligands: ACT.25 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain B: Q.249, R.255 Ligand excluded by PLIP IOD.9: 5 residues within 4Å: Chain B: T.117, C.119, Q.147, H.148, T.160 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain B: H.263 Ligand excluded by PLIP IOD.16: 5 residues within 4Å: Chain A: H.101, Q.103 Chain C: R.272, D.655, M.656 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain C: A.45, P.46, N.47, P.265 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain C: K.411, R.606 Ligand excluded by PLIP IOD.19: 3 residues within 4Å: Chain C: A.7, N.10, P.684 Ligand excluded by PLIP

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

ACT.4: 6 residues within 4Å: Chain A: V.184, T.185, V.186, E.193, T.195, E.198 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.193 Hydrogen bonds: A:V.186, A:E.198 ACT.24: 5 residues within 4Å: Chain C: D.93, K.94, W.215, T.218, D.219 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.94, C:W.215 Water bridges: C:T.218 Salt bridges: C:K.94 ACT.25: 6 residues within 4Å: Chain A: K.97, D.100 Chain C: F.120, M.269, P.271 Ligands: IOD.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:K.97, C:F.120, C:M.269 Hydrogen bonds: A:D.100 Salt bridges: A:K.97

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

CL.5: 1 residues within 4Å: Chain A: H.144 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: P.120, Q.147 Chain C: N.653, G.658 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: N.130, G.135, K.199 Ligand excluded by PLIP CL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: E.403, R.406 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: R.527, Q.542, F.543 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain C: P.619 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain C: P.21, H.22 Ligand excluded by PLIP CL.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.30: 1 residues within 4Å: Chain C: K.620 Ligand excluded by PLIP

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.6: 13 residues within 4Å: Chain B: C.119, Y.121, F.122, C.129, N.130, K.131, C.138, A.140, H.148, A.156, C.157, I.158, A.159 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.119, B:C.129, B:C.138, B:C.157

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.7: 32 residues within 4Å: Chain A: H.101, G.102, Q.103 Chain B: K.26, F.27, I.28, A.29, G.30, G.31, T.32, N.33, L.34, G.98, A.99, L.103, A.107, T.108, A.110, G.111, N.112, L.114, Q.115, P.162, S.163, D.164, E.211, L.212, I.213, K.230, Y.237, A.238, F.239 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:L.103, B:Y.237, B:F.239 Hydrogen bonds: B:K.26, B:F.27, B:A.29, B:G.30, B:G.31, B:T.32, B:T.32, B:N.33, B:L.34, B:N.75, B:A.99, B:T.108, B:N.112, B:Q.115, B:D.164, B:D.164, B:I.213, B:I.213, B:K.230 Water bridges: B:L.114, B:M.165, B:A.240 pi-Stacking: B:F.239 pi-Cation interactions: B:R.118

1 x MCN: PTERIN CYTOSINE DINUCLEOTIDE(Non-covalent)

MCN.14: 36 residues within 4Å: Chain A: Q.157, C.210 Chain C: G.240, G.241, F.242, G.243, R.350, M.465, I.468, G.469, T.470, G.471, S.472, I.475, S.506, G.507, G.508, Q.509, W.510, G.511, A.512, A.613, R.615, I.616, L.617, N.618, T.621, A.622, Q.625, A.687, K.688, G.689, V.690, G.691, E.692 Ligands: MOS.15 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:A.512 Hydrogen bonds: C:G.241, C:F.242, C:G.507, C:G.511, C:A.512, C:R.615, C:L.617, C:N.618, C:T.621, C:Q.625, C:V.690, C:G.691, A:Q.157 Water bridges: C:R.350, C:T.470, C:T.470, C:T.470, C:N.513, A:Q.157

1 x MOS: DIOXOTHIOMOLYBDENUM(VI) ION(Non-covalent)

MOS.15: 12 residues within 4Å: Chain C: Q.211, F.242, G.243, L.246, A.348, M.349, R.350, P.352, G.507, G.508, E.692 Ligands: MCN.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.211, C:G.508

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.26: 3 residues within 4Å: Chain C: W.41, I.234, D.497 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.497, C:D.497 GOL.27: 8 residues within 4Å: Chain C: P.283, T.315, P.316, E.317, T.318, N.347, A.348, P.352 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.318, C:T.318, C:N.347 GOL.28: 6 residues within 4Å: Chain C: I.25, L.29, Y.237, Y.473, A.492, V.493 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.237, C:V.493, C:V.493 Water bridges: C:I.25, C:D.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Correia, M.A. et al., The Escherichia Coli Periplasmic Aldehyde Oxidoreductase is an Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes. Acs Chem.Biol. (2016)

Release Date

2016-09-28

Peptides

Aldehyde oxidoreductase iron-sulfur-binding subunit PaoA: A
Aldehyde oxidoreductase FAD-binding subunit PaoB: B
Aldehyde oxidoreductase molybdenum-binding subunit PaoC: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Aldehyde oxidoreductase iron-sulfur-binding subunit PaoA

Aldehyde oxidoreductase FAD-binding subunit PaoB

Aldehyde oxidoreductase molybdenum-binding subunit PaoC

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