SMTL ID : 3d9f.1

Nitroalkane oxidase: active site mutant S276A crystallized with 1-nitrohexane

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 33 residues within 4Å: Chain A: L.98, L.130, H.132, S.133, G.137, T.138, A.139, N.140, W.168, P.169, S.170, T.239, C.396, L.399, F.400, D.401, G.402, G.403, I.405, G.406, L.407, R.410 Chain B: R.303, I.309, H.312, V.315, K.374, A.375, V.376, G.377, M.378 Chain C: Q.313 Ligands: N6C.2 30 PLIP interactions: 22 interactions with chain A, 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:W.168, A:T.239, A:F.400 Hydrogen bonds: A:L.130, A:H.132, A:S.133, A:S.133, A:S.133, A:T.138, A:A.139, A:N.140, A:S.170, A:F.400, A:D.401, A:G.402, A:G.403, A:G.406, B:K.374, B:M.378, C:Q.313 Water bridges: A:L.399, A:I.405, A:I.405, A:L.407, B:R.303, B:R.303, B:K.379 pi-Stacking: A:F.400, B:H.312 Salt bridges: B:R.303 FAD.5: 34 residues within 4Å: Chain A: R.303, I.309, H.312, V.315, K.374, A.375, V.376, G.377, M.378 Chain B: L.98, L.130, H.132, S.133, G.137, T.138, A.139, N.140, W.168, P.169, S.170, L.233, T.239, F.272, L.399, F.400, D.401, G.402, G.403, I.405, G.406, L.407, R.410 Chain D: Q.313 Ligands: N6C.6 28 PLIP interactions: 21 interactions with chain B, 5 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: B:W.168, B:T.239, B:F.400 Hydrogen bonds: B:L.130, B:H.132, B:S.133, B:S.133, B:S.133, B:T.138, B:A.139, B:N.140, B:S.170, B:L.399, B:F.400, B:D.401, B:G.402, B:G.403, A:K.374, A:M.378, D:Q.313 Water bridges: B:I.405, B:G.406, B:L.407, A:K.379, D:Q.313 pi-Stacking: B:F.400, A:H.312 Salt bridges: A:R.303 FAD.9: 34 residues within 4Å: Chain A: Q.313 Chain C: L.98, L.130, H.132, S.133, G.137, T.138, A.139, N.140, W.168, P.169, S.170, T.239, F.272, C.396, L.399, F.400, D.401, G.402, G.403, I.405, G.406, L.407, R.410 Chain D: R.303, I.309, H.312, V.315, K.374, A.375, V.376, G.377, M.378 Ligands: N6C.10 31 PLIP interactions: 22 interactions with chain C, 1 interactions with chain A, 8 interactions with chain D Hydrophobic interactions: C:T.239, C:F.400 Hydrogen bonds: C:L.130, C:H.132, C:S.133, C:S.133, C:S.133, C:T.138, C:A.139, C:N.140, C:N.140, C:S.170, C:F.400, C:D.401, C:G.402, C:G.403, A:Q.313, D:K.374, D:M.378 Water bridges: C:L.130, C:L.399, C:I.405, C:I.405, C:L.407, D:R.303, D:R.303, D:R.303, D:R.303 pi-Stacking: C:F.400, D:H.312 Salt bridges: D:R.303 FAD.13: 34 residues within 4Å: Chain B: Q.313 Chain C: R.303, I.309, H.312, V.315, K.374, A.375, V.376, G.377, M.378 Chain D: L.98, L.130, H.132, S.133, G.137, T.138, A.139, N.140, W.168, P.169, S.170, L.233, T.239, C.396, L.399, F.400, D.401, G.402, G.403, I.405, G.406, L.407, R.410 Ligands: N6C.14 32 PLIP interactions: 7 interactions with chain C, 23 interactions with chain D, 2 interactions with chain B Hydrogen bonds: C:K.374, C:M.378, D:L.130, D:H.132, D:S.133, D:S.133, D:S.133, D:T.138, D:A.139, D:N.140, D:S.170, D:F.400, D:D.401, D:G.402, D:G.403, D:G.406, B:Q.313 Water bridges: C:R.303, C:R.303, C:K.379, D:L.399, D:I.405, D:I.405, D:L.407, B:Q.313 Salt bridges: C:R.303 pi-Stacking: C:H.312, D:F.400 Hydrophobic interactions: D:W.168, D:L.233, D:T.239, D:F.400

4 x N6C: 1-nitrohexane(Non-covalent)

N6C.2: 8 residues within 4Å: Chain A: V.94, L.98, F.272, A.275, V.279, F.400, D.401 Ligands: FAD.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.98, A:A.275, A:V.279 N6C.6: 8 residues within 4Å: Chain B: V.94, L.98, F.272, V.279, M.282, F.400, D.401 Ligands: FAD.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.94, B:V.279, B:F.400 N6C.10: 8 residues within 4Å: Chain C: V.94, L.98, F.272, A.275, V.279, F.400, D.401 Ligands: FAD.9 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.94, C:L.98, C:A.275, C:V.279, C:F.400 N6C.14: 8 residues within 4Å: Chain D: V.94, L.98, F.272, A.275, V.279, F.400, D.401 Ligands: FAD.13 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.94, D:L.98, D:A.275, D:V.279

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: V.268, E.269, F.272, G.402, L.407, R.408, Q.411 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.268 Water bridges: A:G.402, A:R.408, A:Q.411 GOL.4: 8 residues within 4Å: Chain A: Q.9, S.71, L.72, V.73, H.74, T.338, E.341 Chain C: V.1 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.9, A:S.71, A:L.72, A:V.73, A:H.74, A:E.341, C:V.1, C:V.1 GOL.7: 6 residues within 4Å: Chain B: E.269, F.272, G.402, L.407, R.408, Q.411 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.268, B:Q.411 Water bridges: B:R.408, B:R.408 GOL.8: 7 residues within 4Å: Chain B: Q.9, S.71, L.72, V.73, H.74, E.341 Chain D: V.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.9, B:S.71, B:S.71, B:L.72, B:V.73, B:E.341 GOL.11: 7 residues within 4Å: Chain A: V.1 Chain C: Q.9, S.71, L.72, V.73, H.74, E.341 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.9, C:S.71, C:S.71, C:L.72, C:V.73, C:E.341, A:V.1 GOL.12: 7 residues within 4Å: Chain C: V.268, E.269, F.272, G.402, L.407, R.408, Q.411 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:V.268, C:Q.411, C:Q.411 Water bridges: C:G.402, C:R.408 GOL.15: 6 residues within 4Å: Chain B: V.1 Chain D: Q.9, S.71, L.72, V.73, E.341 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Q.9, D:S.71, D:S.71, D:L.72, D:V.73, D:H.74, D:E.341, B:V.1 GOL.16: 6 residues within 4Å: Chain D: E.269, F.272, G.402, L.407, R.408, Q.411 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.411, D:Q.411 Water bridges: D:Q.265, D:G.402, D:R.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heroux, A. et al., Crystal structures of intermediates in the nitroalkane oxidase reaction. Biochemistry (2009)

Release Date

2009-04-07

Peptides

Nitroalkane oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Nitroalkane oxidase