SMTL ID : 1y5i.2 (1 other biounit)

The crystal structure of the NarGHI mutant NarI-K86A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 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 34 PLIP interactions: 34 interactions with chain A Hydrogen bonds: A:Y.220, A:H.546, A:R.713, A:S.714, A:N.715, A:S.719, A:S.719, A:S.720, A:L.771, A:R.774, A:K.794, A:K.794, A:T.1090, A:H.1092, A:I.1097, A:H.1098, A:S.1099, A:T.1100, A:N.1185, A:N.1185, A:R.1218 Water bridges: A:S.195, A:S.714, A:S.714, A:S.720, A:S.776, A:T.1100, A:T.1100, A:N.1217, A:N.1217 Salt bridges: A:D.772, A:D.822, 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 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:C.53, 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:H.1098 Water bridges: A:T.259, A:D.302, A:D.302, A:R.1218 Salt bridges: A:D.302, A:R.1218 MD1.13: 36 residues within 4Å: Chain D: 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: MD1.14, 6MO.15 32 PLIP interactions: 32 interactions with chain D Hydrogen bonds: D:R.713, D:S.714, D:N.715, D:S.719, D:S.719, D:S.720, D:L.771, D:R.774, D:T.788, D:K.794, D:K.794, D:T.1090, D:H.1092, D:I.1097, D:S.1099, D:T.1100, D:T.1100, D:N.1185, D:N.1185, D:R.1218 Water bridges: D:S.195, D:Y.220, D:S.714, D:S.714, D:S.720, D:S.776, D:N.1217, D:N.1217 Salt bridges: D:D.772, D:D.822, D:H.1098 pi-Stacking: D:F.773 MD1.14: 37 residues within 4Å: Chain D: 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: MD1.13, 6MO.15 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:C.53, D:G.253, D:N.255, D:N.255, D:Q.258, D:T.259, D:R.260, D:V.280, D:D.283, D:G.300, D:A.542, D:G.543, D:H.1092, D:H.1092, D:H.1098 Water bridges: D:D.302, D:D.302, D:R.1218 Salt bridges: D:D.302, D:R.1218

2 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) 6MO.15: 4 residues within 4Å: Chain D: D.222, G.579 Ligands: MD1.13, MD1.14 No protein-ligand interaction detected (PLIP)

8 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: 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 SF4.6: 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 SF4.7: 11 residues within 4Å: Chain B: C.184, E.185, H.186, C.187, P.190, A.191, C.192, 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 SF4.16: 12 residues within 4Å: Chain D: 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 D, Metal complexes: D:H.49, D:C.53, D:C.57, D:C.92 SF4.17: 14 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.16, E:C.19, E:C.22, E:C.263 SF4.18: 12 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.26, E:C.244, E:C.247, E:C.259 SF4.19: 11 residues within 4Å: Chain E: C.184, E.185, H.186, C.187, P.190, A.191, C.192, C.227, Y.229, I.232, K.243 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.184, E:C.187, E:C.192, E:C.227

2 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 F3S.20: 13 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.196, E:C.217, E:C.223

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

3PH.9: 6 residues within 4Å: Chain B: F.491 Chain F: T.123, G.124, A.125, L.197, F.200 7 PLIP interactions: 5 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:L.197, F:F.200, B:F.491, B:F.491 Hydrogen bonds: F:G.124, F:A.125 Water bridges: F:T.123 3PH.21: 6 residues within 4Å: Chain C: T.123, G.124, A.125, L.197, F.200 Chain E: F.491 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:L.197, C:F.200, E:F.491, E:F.491 Hydrogen bonds: C:G.124, C:A.125

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

HEM.10: 22 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, L.108, R.112, L.130, L.133, R.202, L.203, H.205, I.206, V.209 34 PLIP interactions: 29 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:A.37, C:F.55, C:I.59, C:I.59, C:L.60, C:L.108, C:L.133, C:L.203, 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 Metal complexes: C:H.56, C:H.205 HEM.11: 23 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, I.144, M.156, L.159, F.184, H.187, L.188, G.191, M.192, F.195 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:I.59, 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:A.90, 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.187 Metal complexes: C:H.66, C:H.187 HEM.22: 22 residues within 4Å: Chain E: I.88, F.89, W.220, R.221 Chain F: A.37, S.39, S.40, Q.41, M.48, F.55, H.56, I.59, L.60, L.108, R.112, L.130, L.133, R.202, L.203, H.205, I.206, V.209 34 PLIP interactions: 29 interactions with chain F, 5 interactions with chain E, Hydrophobic interactions: F:A.37, F:F.55, F:I.59, F:I.59, F:L.60, F:L.108, F:L.133, F:L.203, F:I.206, F:I.206, F:V.209, E:I.88, E:F.89, E:W.220 Hydrogen bonds: F:S.40, F:Q.41 Water bridges: F:A.38, F:R.111, F:R.112, F:R.112, F:R.112, F:R.202 Salt bridges: F:R.112, F:R.202, E:R.221 pi-Stacking: F:H.56, F:H.56, F:H.56, F:H.205, F:H.205, F:H.205, E:F.89 Metal complexes: F:H.56, F:H.205 HEM.23: 23 residues within 4Å: Chain F: 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, I.144, M.156, L.159, F.184, H.187, L.188, G.191, M.192, F.195 20 PLIP interactions: 20 interactions with chain F, Hydrophobic interactions: F:I.59, F:I.62, F:Q.136, F:L.141, F:I.144, F:L.159, F:F.184, F:F.195 Hydrogen bonds: F:G.94, F:S.147 Water bridges: F:A.90, F:M.156 Salt bridges: F:H.66 pi-Stacking: F:H.66, F:H.66, F:H.187, F:H.187 pi-Cation interactions: F:H.187 Metal complexes: F:H.66, F:H.187

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

AGA.12: 10 residues within 4Å: Chain A: F.3, R.6 Chain B: R.218 Chain C: L.21, S.24, W.25, Y.28, W.35, W.207, S.208 14 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: C:Y.28, C:Y.28, C:W.35, C:W.207, A:F.3, A:F.3 Water bridges: A:R.6, B:S.198, B:K.216 Salt bridges: A:R.6, A:R.6, A:R.6, B:K.216, B:R.218 AGA.24: 10 residues within 4Å: Chain D: F.3, R.6 Chain E: R.218 Chain F: L.21, S.24, W.25, Y.28, W.35, W.207, S.208 15 PLIP interactions: 6 interactions with chain D, 5 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: D:F.3, D:F.3, F:Y.28, F:Y.28, F:W.35, F:W.207 Water bridges: D:R.6, E:S.198, E:K.216 Salt bridges: D:R.6, D:R.6, D:R.6, E:K.216, E:R.218 Hydrogen bonds: F:Y.28

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: AD
Respiratory nitrate reductase 1 beta chain: BE
Respiratory nitrate reductase 1 gamma chain: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

C
C

F
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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