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

Crystal structure of the apomolybdo-NarGHI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 24 residues within 4Å: Chain A: G.50, V.51, F.188, Y.220, W.712, R.713, S.714, N.715, L.716, S.719, S.720, L.771, D.772, F.773, R.774, S.776, T.788, W.791, K.794, D.822, I.1097, H.1098, S.1099, T.1100 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:Y.220, A:R.713, A:N.715, A:L.716, A:S.719, A:S.720, A:S.720, A:L.771, A:L.771, A:R.774, A:R.774, A:S.776, A:K.794, A:S.1099, A:T.1100 Water bridges: A:S.714, A:S.714, A:D.772, A:D.822 Salt bridges: A:D.772, A:D.822, A:H.1098, A:H.1098 pi-Stacking: A:F.773 GDP.11: 24 residues within 4Å: Chain D: G.50, V.51, F.188, Y.220, W.712, R.713, S.714, N.715, L.716, S.719, S.720, L.771, D.772, F.773, R.774, S.776, T.788, W.791, K.794, D.822, I.1097, H.1098, S.1099, T.1100 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:R.713, D:N.715, D:L.716, D:S.719, D:S.720, D:S.720, D:L.771, D:L.771, D:R.774, D:R.774, D:S.776, D:T.788, D:K.794, D:S.1099, D:T.1100, D:T.1100 Water bridges: D:S.714, D:S.714, D:D.822 Salt bridges: D:D.772, D:D.822, D:H.1098, D:H.1098 pi-Stacking: D:F.773

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

SF4.2: 9 residues within 4Å: Chain A: H.49, G.55, S.56, C.57, W.59, G.91, C.92, G.95, Y.1101 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.49, A:C.57, A:C.92, H2O.13 SF4.4: 13 residues within 4Å: Chain B: C.16, I.17, G.18, C.19, H.20, 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 SF4.5: 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 SF4.6: 12 residues within 4Å: Chain B: C.184, E.185, H.186, C.187, P.190, A.191, C.192, C.227, P.228, 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 SF4.12: 9 residues within 4Å: Chain D: H.49, G.55, S.56, C.57, W.59, G.91, C.92, G.95, Y.1101 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.49, D:C.57, D:C.92, H2O.36 SF4.14: 13 residues within 4Å: Chain E: C.16, I.17, G.18, C.19, H.20, 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 SF4.15: 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 SF4.16: 12 residues within 4Å: Chain E: C.184, E.185, H.186, C.187, P.190, A.191, C.192, C.227, P.228, 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

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

3PH.3: 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: 6 interactions with chain C, 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: C:L.21, C:W.25, C:Y.28, C:Y.28, C:W.35, C:W.207, A:F.3, A:F.3 Salt bridges: A:R.6, A:R.6, A:R.6, B:R.218 Water bridges: B:S.198, B:R.218 3PH.8: 1 residues within 4Å: Chain B: F.491 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.491, B:F.491 Water bridges: B:F.491 3PH.13: 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: 3 interactions with chain E, 7 interactions with chain F, 5 interactions with chain D Water bridges: E:S.198, E:R.218 Salt bridges: E:R.218, D:R.6, D:R.6, D:R.6 Hydrophobic interactions: F:L.21, F:W.25, F:Y.28, F:Y.28, F:W.35, F:W.207, D:F.3, D:F.3 Hydrogen bonds: F:Y.28 3PH.18: 1 residues within 4Å: Chain E: F.491 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.491, E:F.491 Water bridges: E:F.491

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

F3S.7: 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 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Ligand interactions Metal complexes: B:C.196, B:C.217, B:C.223, F3S.7, F3S.7, F3S.7 F3S.17: 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 6 PLIP interactions: 3 interactions with chain E, 3 Ligand-Ligand interactions Metal complexes: E:C.196, E:C.217, E:C.223, F3S.17, F3S.17, F3S.17

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

HEM.9: 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.60, R.112, L.130, L.133, R.202, L.203, H.205, I.206, V.209 33 PLIP interactions: 5 interactions with chain B, 28 interactions with chain C, Hydrophobic interactions: B:I.88, B:W.220, B:W.220, C:A.37, C:F.55, C:I.59, C:L.60, C:L.130, C:L.133, C:L.203, C:I.206, 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, C:H.205 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 pi-Cation interactions: C:H.205 Metal complexes: C:H.56, C:H.205 HEM.10: 20 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, S.147, M.156, L.159, H.187, L.188, G.191, M.192, F.195 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:I.59, C:I.62, C:Q.136, C:L.141, C:L.159, C:F.195 Hydrogen bonds: C:G.94, C:S.147 Salt bridges: C:H.66 pi-Stacking: C:H.66, 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 HEM.19: 21 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, R.112, L.130, L.133, R.202, L.203, H.205, I.206, V.209 32 PLIP interactions: 27 interactions with chain F, 5 interactions with chain E, Hydrophobic interactions: F:A.37, F:F.55, F:I.59, F:L.60, F:L.130, F:L.133, F:L.203, F:I.206, F:V.209, E:I.88, E:W.220, E:W.220 Hydrogen bonds: F:S.40, F:Q.41 Water bridges: F:A.38, 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 pi-Cation interactions: F:H.205 Metal complexes: F:H.56, F:H.205 HEM.20: 20 residues within 4Å: Chain F: I.59, I.62, H.66, M.70, A.90, G.94, G.98, L.133, Q.136, C.137, G.140, L.141, S.147, M.156, L.159, H.187, L.188, G.191, M.192, F.195 18 PLIP interactions: 18 interactions with chain F, Hydrophobic interactions: F:I.59, F:I.62, F:Q.136, F:L.141, F:L.159, F:F.195 Hydrogen bonds: F:G.94, F:S.147 Salt bridges: F:H.66 pi-Stacking: F:H.66, F:H.66, F:H.66, F:H.187, F:H.187 pi-Cation interactions: F:H.66, F:H.187 Metal complexes: F:H.66, F:H.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rothery, R.A. et al., The catalytic subunit of Escherichia coli nitrate reductase A contains a novel [4Fe-4S] cluster with a high-spin ground state. Biochemistry (2004)

Release Date

2004-06-08

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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