SMTL ID : 3ir7.6 (5 other biounits)

Crystal structure of NarGHI mutant NarG-R94S

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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.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, N.1218, R.1219 Ligands: MD1.2, 6MO.4 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:Y.221, A:H.547, A:R.714, A:S.715, A:N.716, A:S.720, A:S.720, A:S.721, A:L.772, A:R.775, A:S.777, A:K.795, A:K.795, A:T.1091, A:H.1093, A:I.1098, A:S.1100, A:T.1101, A:N.1186, A:N.1186, A:N.1218, A:R.1219 Water bridges: A:S.715, A:S.715 Salt bridges: A:D.773, A:D.823, A:H.1099, A:H.1099 pi-Stacking: A:F.774 MD1.2: 36 residues within 4Å: Chain A: N.53, C.54, 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, R.1219 Ligands: MD1.1, 6MO.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:C.54, A:G.254, 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:H.1099 Water bridges: A:R.1219 Salt bridges: A:D.303, A:R.1219 MD1.6: 36 residues within 4Å: Chain B: 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, N.1218, R.1219 Ligands: MD1.7, 6MO.9 29 PLIP interactions: 29 interactions with chain B Hydrogen bonds: B:R.714, B:S.715, B:N.716, B:S.720, B:S.720, B:S.721, B:L.772, B:R.775, B:S.777, B:T.789, B:K.795, B:K.795, B:T.1091, B:H.1093, B:I.1098, B:S.1100, B:T.1101, B:T.1101, B:N.1186, B:N.1186, B:N.1218, B:R.1219 Water bridges: B:S.715, B:S.715 Salt bridges: B:D.773, B:D.823, B:H.1099, B:H.1099 pi-Stacking: B:F.774 MD1.7: 36 residues within 4Å: Chain B: N.53, C.54, 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, R.1219 Ligands: MD1.6, 6MO.9 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:C.54, B:G.254, B:N.256, B:Q.259, B:T.260, B:R.261, B:V.281, B:D.284, B:G.301, B:A.543, B:G.544, B:H.1093, B:H.1093, B:H.1099 Water bridges: B:R.1219 Salt bridges: B:D.303, B:R.1219

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

SF4.3: 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 SF4.8: 12 residues within 4Å: Chain B: 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 B, Metal complexes: B:H.50, B:C.54, B:C.58, B:C.93 SF4.11: 13 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.16, C:C.19, C:C.22, C:C.263 SF4.12: 12 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.26, C:C.244, C:C.247, C:C.259 SF4.13: 11 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.184, C:C.187, C:C.192, C:C.227 SF4.17: 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 SF4.18: 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 6MO: MOLYBDENUM(VI) ION(Non-covalent)

6MO.4: 5 residues within 4Å: Chain A: N.53, D.223, G.580 Ligands: MD1.1, MD1.2 No protein-ligand interaction detected (PLIP) 6MO.9: 5 residues within 4Å: Chain B: N.53, D.223, G.580 Ligands: MD1.6, MD1.7 No protein-ligand interaction detected (PLIP)

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

AGA.5: 2 residues within 4Å: Chain A: F.4, R.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.4, A:F.4 Salt bridges: A:R.7, A:R.7, A:R.7 AGA.10: 2 residues within 4Å: Chain B: F.4, R.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.4, B:F.4 Salt bridges: B:R.7, B:R.7, B:R.7

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

F3S.14: 13 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.196, C:C.217, C: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

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

HEM.15: 19 residues within 4Å: Chain C: I.88, F.89, W.220, R.221 Chain D: 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 25 PLIP interactions: 21 interactions with chain D, 4 interactions with chain C, Hydrophobic interactions: D:I.59, D:L.60, D:L.130, D:L.133, D:L.133, D:I.206, D:I.206, D:V.209, C:I.88, C:W.220 Hydrogen bonds: D:S.40, D:Q.41 Salt bridges: D:R.112, D:R.202, C:R.221 pi-Stacking: D:H.56, D:H.56, D:H.56, D:H.205, D:H.205, D:H.205, C:F.89 pi-Cation interactions: D:H.205 Metal complexes: D:H.56, D:H.205 HEM.16: 24 residues within 4Å: Chain D: I.59, I.62, H.66, M.70, A.90, G.94, G.95, G.98, L.133, Q.136, C.137, G.140, L.141, T.143, S.147, M.156, L.159, F.184, H.187, L.188, G.191, M.192, L.194, F.195 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:I.59, D:Q.136, D:L.141, D:L.159, D:F.184, D:L.194, D:F.195 Hydrogen bonds: D:G.94, D:S.147 Salt bridges: D:H.66 pi-Stacking: D:H.66, D:H.66, D:H.187, D:H.187 pi-Cation interactions: D:H.66, D:H.187 Metal complexes: D:H.66, D:H.187 HEM.21: 19 residues within 4Å: Chain E: I.88, F.89, W.220, R.221 Chain F: 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 25 PLIP interactions: 4 interactions with chain E, 21 interactions with chain F, Hydrophobic interactions: E:I.88, E:W.220, F:I.59, F:L.60, F:L.130, F:L.133, F:L.133, F:I.206, F:I.206, F:V.209 Salt bridges: E:R.221, F:R.112, F:R.202 pi-Stacking: E:F.89, F:H.56, F:H.56, F:H.56, F:H.205, F:H.205, F:H.205 Hydrogen bonds: F:S.40, F:Q.41 pi-Cation interactions: F:H.205 Metal complexes: F:H.56, F:H.205 HEM.22: 24 residues within 4Å: Chain F: I.59, I.62, H.66, M.70, A.90, G.94, G.95, G.98, L.133, Q.136, C.137, G.140, L.141, T.143, S.147, M.156, L.159, F.184, H.187, L.188, G.191, M.192, L.194, F.195 18 PLIP interactions: 18 interactions with chain F, Hydrophobic interactions: F:I.59, F:Q.136, F:L.141, F:L.159, F:F.184, F:L.194, 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.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., Protein crystallography reveals a role for the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation. J.Biol.Chem. (2010)

Release Date

2010-01-05

Peptides

Respiratory nitrate reductase 1 alpha chain: AB
Respiratory nitrate reductase 1 beta chain: CE
Respiratory nitrate reductase 1 gamma chain: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

E
B

D
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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