SMTL ID : 2c0u.1

CRYSTAL STRUCTURE OF A COVALENT COMPLEX OF NITROALKANE OXIDASE TRAPPED DURING SUBSTRATE TURNOVER

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: 31 residues within 4Å: Chain A: L.131, H.133, S.134, G.138, T.139, A.140, N.141, W.169, P.170, S.171, T.240, C.397, L.400, F.401, D.402, G.403, G.404, I.406, G.407, R.411 Chain B: R.304, I.310, H.313, V.316, K.375, A.376, V.377, G.378, M.379 Chain C: Q.314 Ligands: NBT.2 31 PLIP interactions: 23 interactions with chain A, 7 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:F.401 Hydrogen bonds: A:L.131, A:H.133, A:S.134, A:S.134, A:S.134, A:S.134, A:T.139, A:A.140, A:N.141, A:N.141, A:S.171, A:L.400, A:F.401, A:D.402, A:G.403, A:G.404, A:G.407, B:K.375, C:Q.314 Water bridges: A:L.131, A:I.406, A:I.406, A:L.408, B:R.304, B:R.304, B:R.304, B:K.380 pi-Stacking: A:F.401, B:H.313 Salt bridges: B:R.304 FAD.3: 32 residues within 4Å: Chain A: R.304, I.310, H.313, V.316, K.375, A.376, V.377, G.378, M.379 Chain B: L.99, L.131, H.133, S.134, G.138, T.139, A.140, N.141, W.169, P.170, S.171, T.240, F.273, C.397, L.400, F.401, D.402, G.403, G.404, I.406, G.407 Chain D: Q.314 Ligands: NBT.4 30 PLIP interactions: 1 interactions with chain D, 23 interactions with chain B, 6 interactions with chain A Hydrogen bonds: D:Q.314, B:L.131, B:H.133, B:S.134, B:S.134, B:S.134, B:S.134, B:T.139, B:A.140, B:N.141, B:S.171, B:L.400, B:F.401, B:D.402, B:G.403, B:G.404, B:G.407, A:K.375 Hydrophobic interactions: B:F.401 Water bridges: B:L.131, B:Q.144, B:I.406, B:I.406, B:L.408, A:R.304, A:R.304, A:K.380 pi-Stacking: B:F.401, A:H.313 Salt bridges: A:R.304 FAD.5: 32 residues within 4Å: Chain A: Q.314 Chain C: L.99, L.131, M.132, H.133, S.134, G.138, T.139, A.140, N.141, W.169, P.170, S.171, T.240, L.400, F.401, D.402, G.403, G.404, I.406, G.407, R.411 Chain D: R.304, I.310, H.313, V.316, K.375, A.376, V.377, G.378, M.379 Ligands: NBT.6 31 PLIP interactions: 24 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:T.240, C:F.401 Hydrogen bonds: C:L.131, C:H.133, C:S.134, C:S.134, C:S.134, C:S.134, C:T.139, C:A.140, C:N.141, C:S.171, C:L.400, C:F.401, C:D.402, C:G.403, C:G.404, C:G.407, D:K.375 Water bridges: C:L.131, C:Q.144, C:I.406, C:L.408, C:L.408, D:R.304, D:R.304, D:R.304, D:K.380 pi-Stacking: C:F.401, D:H.313 Salt bridges: D:R.304 FAD.7: 32 residues within 4Å: Chain B: Q.314 Chain C: R.304, I.310, H.313, V.316, K.375, A.376, V.377, G.378, M.379 Chain D: L.99, L.131, H.133, S.134, G.138, T.139, A.140, N.141, W.169, P.170, S.171, C.397, L.400, F.401, D.402, G.403, G.404, I.406, G.407, L.408, R.411 Ligands: NBT.8 31 PLIP interactions: 23 interactions with chain D, 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: D:F.401 Hydrogen bonds: D:L.131, D:H.133, D:S.134, D:S.134, D:S.134, D:S.134, D:T.139, D:A.140, D:N.141, D:N.141, D:S.171, D:L.400, D:F.401, D:D.402, D:G.403, D:G.404, D:G.407, C:K.375, B:Q.314 Water bridges: D:L.131, D:I.406, D:I.406, D:L.408, C:R.304, C:R.304, C:R.304, C:K.380 pi-Stacking: D:F.401, C:H.313 Salt bridges: C:R.304

4 x NBT: (2S)-2-NITROBUTANE(Non-covalent)

NBT.2: 9 residues within 4Å: Chain A: I.92, V.95, A.96, L.99, S.171, S.276, F.401, D.402 Ligands: FAD.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.96, A:F.401, A:D.402 NBT.4: 9 residues within 4Å: Chain B: I.92, V.95, A.96, L.99, S.171, M.283, F.401, D.402 Ligands: FAD.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.96, B:F.401, B:D.402 NBT.6: 8 residues within 4Å: Chain C: V.95, A.96, L.99, S.171, S.276, F.401, D.402 Ligands: FAD.5 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.96, C:F.401, C:D.402 NBT.8: 7 residues within 4Å: Chain D: V.95, A.96, L.99, S.171, F.401, D.402 Ligands: FAD.7 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.96, D:F.401, D:D.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagpal, A. et al., Crystal Structures of Nitroalkane Oxidase: Insights Into the Reaction Mechanism from a Covalent Complex of the Flavoenzyme Trapped During Turnover. Biochemistry (2006)

Release Date

2006-02-01

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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