SMTL ID : 1r27.4 (4 other biounits)

Crystal Structure of NarGH complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-4-4-mer

Ligands

4 x MO: MOLYBDENUM ATOM(Non-covalent)

MO.1: 5 residues within 4Å: Chain A: N.52, D.222, G.579 Ligands: MGD.3, MGD.4 Ligand excluded by PLIP MO.9: 5 residues within 4Å: Chain C: N.52, D.222, G.579 Ligands: MGD.11, MGD.12 Ligand excluded by PLIP MO.17: 6 residues within 4Å: Chain E: N.52, D.222, G.579, H.1098 Ligands: MGD.19, MGD.20 Ligand excluded by PLIP MO.25: 6 residues within 4Å: Chain G: N.52, D.222, G.579, H.1098 Ligands: MGD.27, MGD.28 Ligand excluded by PLIP

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

SF4.2: 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 SF4.6: 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: 11 residues within 4Å: Chain B: C.184, E.185, H.186, C.187, 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 SF4.8: 13 residues within 4Å: Chain B: C.16, I.17, G.18, C.19, H.20, T.21, C.22, 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 SF4.10: 12 residues within 4Å: Chain C: 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 C, Metal complexes: C:H.49, C:C.53, C:C.57, C:C.92 SF4.14: 11 residues within 4Å: Chain D: 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 D, Metal complexes: D:C.26, D:C.244, D:C.247, D:C.259 SF4.15: 11 residues within 4Å: Chain D: C.184, E.185, H.186, C.187, A.191, C.192, V.210, C.227, Y.229, I.232, K.243 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.184, D:C.187, D:C.192, D:C.227 SF4.16: 13 residues within 4Å: Chain D: C.16, I.17, G.18, C.19, H.20, T.21, C.22, P.181, C.263, V.264, G.265, I.267, R.268 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.16, D:C.19, D:C.22, D:C.263 SF4.18: 12 residues within 4Å: Chain E: 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 E, Metal complexes: E:H.49, E:C.53, E:C.57, E:C.92 SF4.22: 11 residues within 4Å: Chain F: 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 F, Metal complexes: F:C.26, F:C.244, F:C.247, F:C.259 SF4.23: 11 residues within 4Å: Chain F: C.184, E.185, H.186, C.187, A.191, C.192, V.210, C.227, Y.229, I.232, K.243 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.184, F:C.187, F:C.192, F:C.227 SF4.24: 13 residues within 4Å: Chain F: C.16, I.17, G.18, C.19, H.20, T.21, C.22, P.181, C.263, V.264, G.265, I.267, R.268 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.16, F:C.19, F:C.22, F:C.263 SF4.26: 12 residues within 4Å: Chain G: 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 G, Metal complexes: G:H.49, G:C.53, G:C.57, G:C.92 SF4.30: 11 residues within 4Å: Chain H: 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 H, Metal complexes: H:C.26, H:C.244, H:C.247, H:C.259 SF4.31: 11 residues within 4Å: Chain H: C.184, E.185, H.186, C.187, A.191, C.192, V.210, C.227, Y.229, I.232, K.243 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.184, H:C.187, H:C.192, H:C.227 SF4.32: 13 residues within 4Å: Chain H: C.16, I.17, G.18, C.19, H.20, T.21, C.22, P.181, C.263, V.264, G.265, I.267, R.268 4 PLIP interactions: 4 interactions with chain H, Metal complexes: H:C.16, H:C.19, H:C.22, H:C.263

8 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.3: 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, L.716, 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, N.1217, R.1218 Ligands: MO.1, MGD.4 31 PLIP interactions: 31 interactions with chain A Hydrogen bonds: A:R.713, A:N.715, A:S.720, A:K.722, A:L.771, A:R.774, A:R.774, A:K.794, A:K.794, A:T.1090, A:T.1090, A:H.1092, A:S.1099, A:T.1100, A:T.1100, A:N.1185, A:N.1185, A:R.1218 Water bridges: A:N.52, A:S.195, A:Y.220, A:Y.220, A:S.714, A:S.714, A:N.715, A:S.720 Salt bridges: A:D.772, A:D.822, A:H.1098, A:H.1098 pi-Stacking: A:H.1163 MGD.4: 36 residues within 4Å: Chain A: N.52, 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: MO.1, MGD.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.255, A:Q.258, A:T.259, A:T.259, A:R.260, A:V.280, A:D.283, A:G.300, A:A.542, A:G.543, A:H.1092, A:H.1092, A:G.1096, A:H.1098, A:H.1098 Water bridges: A:N.255, A:N.255, A:D.302, A:D.302 Salt bridges: A:D.302, A:R.1218 MGD.11: 36 residues within 4Å: Chain C: G.50, N.52, P.190, Y.220, D.222, H.546, W.712, R.713, S.714, N.715, L.716, 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, N.1217, R.1218 Ligands: MO.9, MGD.12 31 PLIP interactions: 31 interactions with chain C Hydrogen bonds: C:R.713, C:N.715, C:S.720, C:K.722, C:L.771, C:R.774, C:R.774, C:K.794, C:K.794, C:T.1090, C:T.1090, C:H.1092, C:S.1099, C:T.1100, C:T.1100, C:N.1185, C:N.1185, C:R.1218 Water bridges: C:N.52, C:S.195, C:Y.220, C:Y.220, C:S.714, C:S.714, C:N.715, C:S.720 Salt bridges: C:D.772, C:D.822, C:H.1098, C:H.1098 pi-Stacking: C:H.1163 MGD.12: 36 residues within 4Å: Chain C: N.52, 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: MO.9, MGD.11 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:N.255, C:Q.258, C:T.259, C:T.259, C:R.260, C:V.280, C:D.283, C:G.300, C:A.542, C:G.543, C:H.1092, C:H.1092, C:G.1096, C:H.1098, C:H.1098 Water bridges: C:N.255, C:N.255, C:D.302, C:D.302 Salt bridges: C:D.302, C:R.1218 MGD.19: 35 residues within 4Å: Chain E: G.50, N.52, P.190, Y.220, D.222, H.546, W.712, R.713, S.714, N.715, L.716, 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, N.1217, R.1218 Ligands: MO.17, MGD.20 32 PLIP interactions: 32 interactions with chain E Hydrogen bonds: E:H.546, E:R.713, E:N.715, E:S.720, E:L.771, E:R.774, E:R.774, E:T.788, E:K.794, E:K.794, E:T.1090, E:T.1090, E:H.1092, E:S.1099, E:T.1100, E:H.1163, E:N.1185, E:N.1185, E:R.1218 Water bridges: E:S.195, E:S.720, E:S.720, E:D.772, E:D.772, E:D.772, E:T.1100, E:T.1100 Salt bridges: E:D.772, E:D.822, E:H.1098, E:H.1098 pi-Stacking: E:F.773 MGD.20: 36 residues within 4Å: Chain E: N.52, 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: MO.17, MGD.19 19 PLIP interactions: 19 interactions with chain E Hydrogen bonds: E:G.253, E:N.255, E:N.255, E:Q.258, E:T.259, E:R.260, E:V.280, E:D.283, E:G.300, E:A.542, E:G.543, E:H.1092, E:H.1092, E:G.1096, E:H.1098 Water bridges: E:D.302, E:W.547 Salt bridges: E:D.302, E:R.1218 MGD.27: 35 residues within 4Å: Chain G: G.50, N.52, P.190, Y.220, D.222, H.546, W.712, R.713, S.714, N.715, L.716, 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, N.1217, R.1218 Ligands: MO.25, MGD.28 32 PLIP interactions: 32 interactions with chain G Hydrogen bonds: G:H.546, G:R.713, G:N.715, G:S.720, G:L.771, G:R.774, G:R.774, G:T.788, G:K.794, G:K.794, G:T.1090, G:T.1090, G:H.1092, G:S.1099, G:T.1100, G:H.1163, G:N.1185, G:N.1185, G:R.1218 Water bridges: G:S.195, G:S.720, G:S.720, G:D.772, G:D.772, G:D.772, G:T.1100, G:T.1100 Salt bridges: G:D.772, G:D.822, G:H.1098, G:H.1098 pi-Stacking: G:F.773 MGD.28: 36 residues within 4Å: Chain G: N.52, 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: MO.25, MGD.27 19 PLIP interactions: 19 interactions with chain G Hydrogen bonds: G:G.253, G:N.255, G:N.255, G:Q.258, G:T.259, G:R.260, G:V.280, G:D.283, G:G.300, G:A.542, G:G.543, G:H.1092, G:H.1092, G:G.1096, G:H.1098 Water bridges: G:D.302, G:W.547 Salt bridges: G:D.302, G:R.1218

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

F3S.5: 11 residues within 4Å: Chain B: C.196, 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.13: 11 residues within 4Å: Chain D: C.196, 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 D, Metal complexes: D:C.196, D:C.217, D:C.223 F3S.21: 12 residues within 4Å: Chain F: C.196, A.200, 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 F, Metal complexes: F:C.196, F:C.217, F:C.223 F3S.29: 12 residues within 4Å: Chain H: C.196, A.200, 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 H, Metal complexes: H:C.196, H:C.217, H:C.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jormakka, M. et al., Architecture of NarGH reveals a structural classification of Mo-bisMGD enzymes. Structure (2004)

Release Date

2004-02-17

Peptides

Respiratory nitrate reductase 1 alpha chain: ACEG
Respiratory nitrate reductase 1 beta chain: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
C

G
C

B
B

D
B

F
D

H
D

Respiratory nitrate reductase 1 alpha chain

Respiratory nitrate reductase 1 beta chain

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