SMTL ID : 1q16.1 (3 other biounits)

Crystal structure of Nitrate Reductase A, NarGHI, from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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: 37 residues within 4Å: Chain A: G.51, N.53, P.191, Y.221, D.223, H.547, W.713, R.714, S.715, N.716, L.717, S.720, S.721, K.723, L.772, D.773, F.774, R.775, S.777, T.789, W.792, K.795, D.823, T.1091, H.1093, I.1098, H.1099, S.1100, T.1101, H.1164, H.1185, N.1186, T.1189, N.1218, R.1219 Ligands: MD1.2, 6MO.3 34 PLIP interactions: 34 interactions with chain A Hydrogen bonds: A:Y.221, A:H.547, A:R.714, A:R.714, A:N.716, A:S.720, A:S.720, A:S.720, A:L.772, A:R.775, A:S.777, A:K.795, A:K.795, A:T.1091, A:T.1091, A:H.1093, A:S.1100, A:T.1101, A:H.1164, A:N.1186, A:N.1186, A:R.1219 Water bridges: A:S.196, A:S.715, A:S.715, A:S.721, A:K.723, A:D.773, A:N.1218 Salt bridges: A:D.773, A:D.823, A:H.1099, A:H.1099 pi-Stacking: A:F.774 MD1.2: 38 residues within 4Å: Chain A: N.53, C.54, R.95, D.223, W.253, G.254, S.255, N.256, Q.259, T.260, R.261, V.281, T.282, P.283, D.284, A.286, Q.300, G.301, D.303, G.542, A.543, G.544, L.545, W.548, Y.578, V.579, G.580, L.1090, P.1092, H.1093, Q.1094, G.1097, I.1098, H.1099, H.1164, R.1219 Ligands: MD1.1, 6MO.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.254, A:G.254, A:N.256, A:N.256, A:Q.259, A:R.261, A:V.281, A:D.284, A:G.301, A:A.543, A:G.544, A:H.1093, A:G.1097, A:H.1099, A:H.1099 Water bridges: A:T.260, A:D.303, A:D.303 Salt bridges: A:D.303, A:R.1219

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

6MO.3: 5 residues within 4Å: Chain A: N.53, D.223, G.580 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.50, V.52, C.54, G.56, S.57, C.58, W.60, G.92, C.93, G.96, P.263, Y.1102 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.50, A:C.54, A:C.58, A:C.93 SF4.6: 14 residues within 4Å: Chain B: C.16, I.17, G.18, 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 SF4.7: 12 residues within 4Å: Chain B: C.26, W.30, F.41, 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 SF4.8: 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 AGA: (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE(Non-covalent)

AGA.5: 18 residues within 4Å: Chain A: F.4, R.7, Y.10 Chain B: P.197, S.198, K.216, R.218 Chain C: L.21, S.24, W.25, Y.28, W.35, W.207, S.208, V.209, P.210, V.211, E.212 16 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: C:Y.28, C:Y.28, C:W.35, A:F.4, A:F.4 Hydrogen bonds: C:V.209, C:E.212, C:E.212, A:Y.10 Water bridges: C:Y.213, B:R.218 Salt bridges: B:K.216, B:R.218, A:R.7, A:R.7, A:R.7

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

F3S.9: 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.10: 1 residues within 4Å: Chain B: F.491 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.491, B:F.491

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

HEM.11: 20 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.60, R.112, L.130, L.133, R.202, H.205, I.206, V.209 33 PLIP interactions: 28 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:A.37, C:I.59, C:I.59, C:L.60, C:L.130, C:L.133, C:I.206, C:I.206, C:V.209, B:I.88, B:F.89, B:W.220 Hydrogen bonds: C:S.40, C:Q.41 Water bridges: C:A.38, C:R.111, C:R.112, C:R.112, C:R.112, C:R.202 Salt bridges: C:R.112, C:R.202, B:R.221 pi-Stacking: C:H.56, C:H.56, C:H.56, C:H.205, C:H.205, C:H.205, B:F.89 pi-Cation interactions: C:H.205 Metal complexes: C:H.56, C:H.205 HEM.12: 24 residues within 4Å: Chain C: I.59, I.62, H.66, M.70, Q.87, A.90, G.94, G.95, G.98, L.133, Q.136, C.137, G.140, L.141, T.143, I.144, M.156, L.159, F.184, H.187, L.188, G.191, M.192, F.195 23 PLIP interactions: 23 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:G.94, C:S.147 Water bridges: C:S.147, C:M.156 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, C:H.187 Metal complexes: C:H.66, C:H.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertero, M.G. et al., Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A. Nat.Struct.Biol. (2003)

Release Date

2003-10-07

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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