SMTL ID : 3fcj.1

Nitroalkane oxidase: mutant402N crystallized with nitroethane

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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, L.233, 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: NIE.2 30 PLIP interactions: 21 interactions with chain A, 1 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: A:W.168, A:L.233 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, C:Q.313, B:K.374, B:M.378 Water bridges: A:L.399, A:I.405, A:I.405, A:L.407, B:R.303, B:R.303, B:R.303, B:K.379 Salt bridges: B:R.303 pi-Stacking: B:H.312 FAD.5: 35 residues within 4Å: Chain A: R.303, I.309, H.312, V.315, K.374, A.375, V.376, G.377, M.378, Y.381 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, N.401, G.402, G.403, I.405, G.406, L.407, R.410 Chain D: Q.313 Ligands: NIE.6 26 PLIP interactions: 19 interactions with chain B, 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: B:W.168, B:T.239, A:Y.381 Hydrogen bonds: B:L.130, B:H.132, B:S.133, B:S.133, B:T.138, B:A.139, B:N.140, B:W.168, B:S.170, B:F.400, 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 Salt bridges: A:R.303 pi-Stacking: A:H.312 FAD.8: 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, T.239, 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: NIE.9 27 PLIP interactions: 7 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:S.170, C:F.400, C:N.401, C:G.402, C:G.403, A:Q.313 Water bridges: D:R.303, D:R.303, D:R.303, 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:W.168 FAD.12: 33 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, T.239, C.396, L.399, F.400, N.401, G.402, G.403, I.405, G.406, L.407, R.410 Ligands: NIE.13 29 PLIP interactions: 21 interactions with chain D, 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:W.168, D:T.239, 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:L.399, D:F.400, D:G.402, D:G.403, D:G.406, C:K.374, C:M.378, B:Q.313 Water bridges: D:I.405, D:I.405, D:L.407, C:R.303, C:R.303, C:R.303 pi-Stacking: D:F.400, C:H.312 Salt bridges: C:R.303

4 x NIE: nitroethane(Non-covalent)

NIE.2: 5 residues within 4Å: Chain A: V.94, L.98, F.400, N.401 Ligands: FAD.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.94 NIE.6: 5 residues within 4Å: Chain B: L.98, F.272, F.400, N.401 Ligands: FAD.5 No protein-ligand interaction detected (PLIP) NIE.9: 4 residues within 4Å: Chain C: L.98, F.400, N.401 Ligands: FAD.8 No protein-ligand interaction detected (PLIP) NIE.13: 5 residues within 4Å: Chain D: L.98, F.272, F.400, N.401 Ligands: FAD.12 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.400

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: E.269, F.272, G.402, L.407, R.408, Q.411 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.411, A:Q.411 Water bridges: A:Q.265, A:R.408 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: 2 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:V.1, C:V.1, A:Q.9, A:S.71, A:L.72, A:V.73, A:H.74, A:E.341 GOL.7: 6 residues within 4Å: Chain B: E.269, F.272, G.402, L.407, R.408, Q.411 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.411, B:Q.411 Water bridges: B:R.408 GOL.10: 6 residues within 4Å: Chain C: E.269, F.272, G.402, L.407, R.408, Q.411 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.411, C:Q.411 Water bridges: C:Q.265, C:R.408 GOL.11: 7 residues within 4Å: Chain A: V.1 Chain C: Q.9, S.71, V.73, H.74, T.338, E.341 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.9, C:S.71, C:S.71, C:V.73, C:T.338, C:E.341 GOL.14: 6 residues within 4Å: Chain D: E.269, F.272, G.402, L.407, R.408, Q.411 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.411, D:Q.411 Water bridges: D:R.408

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Major, D.T. et al., Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-11-03

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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