SMTL ID : 3d9e.1

Nitroalkane oxidase: active site mutant D402N crystallized with 1-nitrooctane

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 32 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, C.396, L.399, F.400, N.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: N8C.2 30 PLIP interactions: 21 interactions with chain A, 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:F.400, 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:N.140, A:S.170, A:F.400, A:N.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:R.303, B:R.303 Salt bridges: B:R.303 pi-Stacking: B:H.312 FAD.4: 33 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, F.272, C.396, L.399, F.400, N.401, G.402, G.403, I.405, G.406, L.407, R.410 Chain D: Q.313 Ligands: N8C.5 26 PLIP interactions: 20 interactions with chain B, 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:W.168, 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:N.401, B:G.402, B:G.403, A:K.374, A:M.378, D:Q.313 Water bridges: B:L.399, B:I.405, B:G.406, B:L.407, A:K.379 pi-Stacking: B:F.400, A:H.312 Salt bridges: A:R.303 FAD.7: 33 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, F.272, C.396, L.399, F.400, N.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: N8C.8 28 PLIP interactions: 8 interactions with chain D, 19 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:K.374, D:M.378, 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:G.402, C:G.403, A:Q.313 Water bridges: D:R.303, D:R.303, D:R.303, D:K.379, C:L.399, C:I.405, C:G.406, C:L.407 Salt bridges: D:R.303 pi-Stacking: D:H.312, C:F.400 Hydrophobic interactions: C:F.400 FAD.10: 32 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, C.396, L.399, F.400, N.401, G.402, G.403, I.405, G.406, L.407, R.410 Ligands: N8C.11 30 PLIP interactions: 20 interactions with chain D, 8 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: D:W.168, D:F.400 Hydrogen bonds: 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:N.401, D:G.402, D:G.403, D:G.406, C:K.374, C:M.378, B:Q.313 Water bridges: D:L.399, D:I.405, D:I.405, D:L.407, C:R.303, C:R.303, C:R.303, C:R.303, B:Q.313 Salt bridges: C:R.303 pi-Stacking: C:H.312

4 x N8C: 1-nitrooctane(Non-covalent)

N8C.2: 8 residues within 4Å: Chain A: V.94, A.95, L.98, F.272, S.275, F.400, N.401 Ligands: FAD.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.94, A:V.94, A:F.400 N8C.5: 8 residues within 4Å: Chain B: V.94, L.98, F.272, S.275, V.279, F.400, N.401 Ligands: FAD.4 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.94, B:L.98, B:V.279, B:F.400 N8C.8: 9 residues within 4Å: Chain C: V.94, L.98, F.272, S.275, L.278, V.279, F.400, N.401 Ligands: FAD.7 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.94, C:L.278, C:V.279, C:F.400 N8C.11: 10 residues within 4Å: Chain D: V.94, L.98, F.272, S.275, L.278, V.279, M.282, F.400, N.401 Ligands: FAD.10 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:V.94, D:V.94, D:L.278, D:F.400

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: W.141, E.269, F.272, G.402, L.407, R.408, Q.411 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.268, A:Q.411 Water bridges: A:G.402, A:R.408, A:R.408 GOL.6: 6 residues within 4Å: Chain B: E.269, F.272, G.402, L.407, R.408, Q.411 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.268, B:Q.411, B:Q.411 Water bridges: B:Q.265, B:G.402 GOL.9: 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.12: 6 residues within 4Å: Chain D: E.269, F.272, G.402, L.407, R.408, Q.411 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.411, D:Q.411

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

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