SMTL ID : 1y5n.1 (1 other biounit)

The crystal structure of the NarGHI mutant NarI-K86A in complex with pentachlorophenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x MD1: PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER(Non-covalent)

MD1.1: 36 residues within 4Å: Chain A: G.50, N.52, P.190, Y.220, D.222, H.546, W.712, R.713, S.714, N.715, S.719, S.720, K.722, L.771, D.772, F.773, R.774, S.776, T.788, W.791, K.794, D.822, T.1090, H.1092, I.1097, H.1098, S.1099, T.1100, H.1163, H.1184, N.1185, T.1188, N.1217, R.1218 Ligands: MD1.2, 6MO.3 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:Y.220, A:H.546, A:R.713, A:R.713, A:N.715, A:S.719, A:S.719, A:S.719, A:K.722, A:L.771, A:R.774, A:S.776, A:K.794, A:K.794, A:T.1090, A:T.1090, A:H.1092, A:S.1099, A:T.1100, A:N.1185, A:N.1185, A:N.1217, A:R.1218 Salt bridges: A:D.822, A:H.1098, A:H.1098 pi-Stacking: A:F.773 MD1.2: 37 residues within 4Å: Chain A: N.52, C.53, R.94, D.222, W.252, G.253, S.254, N.255, Q.258, T.259, R.260, V.280, T.281, P.282, D.283, A.285, Q.299, G.300, D.302, G.541, A.542, G.543, L.544, W.547, Y.577, V.578, G.579, L.1089, P.1091, H.1092, Q.1093, G.1096, I.1097, H.1098, R.1218 Ligands: MD1.1, 6MO.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.253, A:G.253, A:N.255, A:N.255, A:Q.258, A:R.260, A:V.280, A:D.283, A:G.300, A:A.542, A:G.543, A:H.1092, A:G.1096, A:H.1098, A:H.1098 Salt bridges: A:D.302, A:R.1218

1 x 6MO: MOLYBDENUM(VI) ION(Non-covalent)

6MO.3: 4 residues within 4Å: Chain A: D.222, G.579 Ligands: MD1.1, MD1.2 No protein-ligand interaction detected (PLIP)

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

SF4.4: 12 residues within 4Å: Chain A: H.49, V.51, C.53, G.55, S.56, C.57, W.59, G.91, C.92, G.95, P.262, Y.1101 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.49, A:C.53, A:C.57, A:C.92 SF4.5: 13 residues within 4Å: Chain B: C.16, I.17, C.19, H.20, T.21, C.22, V.44, P.181, C.263, V.264, G.265, I.267, R.268 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.16, B:C.19, B:C.22, B:C.263 SF4.6: 11 residues within 4Å: Chain B: C.26, W.30, N.42, L.183, C.244, I.245, F.246, C.247, T.257, V.258, C.259 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.26, B:C.244, B:C.247, B:C.259 SF4.7: 12 residues within 4Å: Chain B: C.184, E.185, H.186, C.187, P.190, A.191, C.192, V.210, C.227, Y.229, I.232, K.243 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.184, B:C.187, B:C.192, B:C.227

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.8: 13 residues within 4Å: Chain B: C.196, P.197, S.198, I.201, I.212, C.217, R.218, G.219, W.220, R.221, M.222, C.223, S.241 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.196, B:C.217, B:C.223

1 x 3PH: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE(Non-covalent)

3PH.9: 2 residues within 4Å: Chain B: F.491, L.493 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.491, B:L.493

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.10: 21 residues within 4Å: Chain B: I.88, F.89, W.220, R.221 Chain C: A.37, S.39, S.40, Q.41, M.48, F.55, H.56, I.59, L.108, R.112, L.130, L.133, R.202, L.203, H.205, I.206, V.209 27 PLIP interactions: 4 interactions with chain B, 23 interactions with chain C, Hydrophobic interactions: B:I.88, B:W.220, C:A.37, C:F.55, C:I.59, C:L.108, C:L.130, C:L.133, C:L.203, C:I.206, C:V.209, C:V.209 Salt bridges: B:R.221, C:R.112, C:R.202 pi-Stacking: B:F.89, C:H.56, C:H.56, C:H.56, C:H.205, C:H.205 Hydrogen bonds: C:S.40, C:S.40, C:Q.41 pi-Cation interactions: C:H.205 Metal complexes: C:H.56, C:H.205 HEM.11: 24 residues within 4Å: Chain C: I.59, I.62, H.66, M.70, A.90, G.94, G.98, L.133, Q.136, C.137, G.140, L.141, T.143, I.144, S.147, M.156, L.159, F.184, H.187, L.188, G.191, M.192, F.195 Ligands: PCI.13 19 PLIP interactions: 19 interactions with chain C, Hydrophobic interactions: C:I.59, C:I.62, C:I.62, C:Q.136, C:L.141, C:I.144, C:L.159, C:F.184, C:F.195 Hydrogen bonds: C:S.147 Salt bridges: C:H.66 pi-Stacking: C:H.66, C:H.66, C:H.187, C:H.187 pi-Cation interactions: C:H.66, C:H.187 Metal complexes: C:H.66, C:H.187

1 x AGA: (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE(Non-covalent)

AGA.12: 14 residues within 4Å: Chain A: F.3, R.6 Chain B: S.198, K.216, R.218 Chain C: S.24, W.25, Y.28, W.35, W.207, S.208, V.209, P.210, E.212 17 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: C:W.25, C:W.25, C:Y.28, C:Y.28, C:W.35, C:W.207, A:F.3, A:F.3 Hydrogen bonds: C:E.212, C:E.212, C:E.212, A:Y.9 Salt bridges: B:K.216, B:R.218, A:R.6, A:R.6, A:R.6

1 x PCI: PENTACHLOROPHENOL(Non-covalent)

PCI.13: 8 residues within 4Å: Chain C: G.65, H.66, G.69, M.70, A.86, A.90, M.156 Ligands: HEM.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertero, M.G. et al., Structural and Biochemical Characterization of a Quinol Binding Site of Escherichia coli Nitrate Reductase A. J.Biol.Chem. (2005)

Release Date

2005-03-08

Peptides

Respiratory nitrate reductase 1 alpha chain: A
Respiratory nitrate reductase 1 beta chain: B
Respiratory nitrate reductase 1 gamma chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Respiratory nitrate reductase 1 alpha chain

Respiratory nitrate reductase 1 beta chain

Respiratory nitrate reductase 1 gamma chain

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