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

CYTOCHROME C NITRITE REDUCTASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.175, Y.176, Y.219, K.238, Q.240 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.175, A:Y.176, A:K.238, H2O.2, H2O.2 CA.10: 5 residues within 4Å: Chain B: E.175, Y.176, Y.219, K.238, Q.240 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.175, B:Y.176, B:K.238, H2O.25, H2O.25

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: F.50, R.72, K.92, Y.176, Q.240, H.241 Ligands: HEC.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.176, A:Y.176, A:Y.176 Water bridges: A:R.72, A:R.72, A:Q.240, A:Q.240 Salt bridges: A:R.72, A:K.92, A:H.241 SO4.3: 4 residues within 4Å: Chain A: N.209, R.377 Chain B: E.311, F.315 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.209 Water bridges: A:E.213, A:R.377, A:R.377 Salt bridges: A:R.377 SO4.4: 3 residues within 4Å: Chain A: K.326, R.390 Chain B: K.388 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Water bridges: A:Q.387, A:R.390, A:R.390, A:R.390, B:K.388, B:K.388 Salt bridges: A:K.326, A:R.390, B:K.388 SO4.11: 7 residues within 4Å: Chain B: F.50, R.72, K.92, Y.176, Q.240, H.241 Ligands: HEC.14 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.176, B:Y.176, B:Y.176 Water bridges: B:R.72, B:R.72, B:Q.240, B:Q.240 Salt bridges: B:R.72, B:K.92, B:H.241 SO4.12: 4 residues within 4Å: Chain A: E.311, F.315 Chain B: N.209, R.377 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.209 Water bridges: B:E.213, B:R.377, B:R.377 Salt bridges: B:R.377 SO4.13: 3 residues within 4Å: Chain A: K.388 Chain B: K.326, R.390 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Water bridges: B:Q.387, B:R.390, B:R.390, B:R.390, A:K.388, A:K.388 Salt bridges: B:K.326, B:R.390, A:K.388

10 x HEC: HEME C(Covalent)

HEC.5: 23 residues within 4Å: Chain A: Y.54, N.55, P.57, D.66, N.67, S.70, R.72, T.73, L.84, A.87, C.88, C.91, K.92, C.172, H.173, Y.176, F.178, V.196, H.241, A.363, H.365 Ligands: SO4.2, HEC.7 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:P.57, A:T.73, A:L.84, A:Y.176, A:Y.176, A:Y.176, A:F.178, A:V.196, A:H.241 Hydrogen bonds: A:N.55, A:N.55, A:A.363 Water bridges: A:Y.54, A:Y.54, A:R.72, A:H.365 Salt bridges: A:R.72, A:H.241, A:H.365 pi-Stacking: A:H.241 HEC.6: 19 residues within 4Å: Chain A: W.11, Y.15, Q.18, F.19, W.22, G.125, C.126, C.129, H.130, L.137, H.161, R.165, V.168, M.264, Y.266, Y.274, S.275, H.277 Ligands: HEC.7 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:W.11, A:Y.15, A:Y.15, A:Q.18, A:F.19, A:W.22, A:L.137, A:V.168 Hydrogen bonds: A:S.275 Salt bridges: A:H.161, A:R.165, A:H.277 Metal complexes: A:H.130, A:H.277 HEC.7: 27 residues within 4Å: Chain A: T.25, Y.28, P.57, R.58, G.59, H.60, Y.62, A.63, D.66, C.91, K.92, I.124, N.128, V.168, C.169, Q.171, C.172, H.173, C.259, H.263, M.264, V.279, K.280, E.281 Ligands: HEC.5, HEC.6, HEC.8 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:K.92, A:Q.171, A:H.263 Hydrogen bonds: A:R.58, A:H.60, A:Y.62 Salt bridges: A:H.60 Metal complexes: A:H.60, A:H.173 HEC.8: 23 residues within 4Å: Chain A: P.57, T.166, C.169, H.173, F.244, W.247, H.252, V.257, S.258, C.259, C.262, H.263, E.281, N.282, P.283, L.284, H.365, G.366, Y.368, F.369, H.370 Ligands: HEC.7, HEC.9 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:T.166, A:H.173, A:W.247, A:L.284, A:F.369, A:F.369 Hydrogen bonds: A:E.281 Water bridges: A:E.281, A:N.282, A:N.282, A:H.365 Metal complexes: A:H.263, A:H.370 HEC.9: 22 residues within 4Å: Chain A: I.251, H.252, K.255, V.257, C.262, P.283, L.284, S.290, C.291, N.293, C.294, H.295, L.302, I.305, V.306, K.309, F.369, P.372 Chain B: I.251, H.295 Ligands: HEC.8, HEC.18 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:I.251, A:I.251, A:K.255, A:V.257, A:V.257, A:P.283, A:L.284, A:L.302, A:L.302, A:I.305, A:V.306, A:F.369, B:I.251 Water bridges: A:K.255, A:H.295, A:K.309, B:C.294, B:H.295 Salt bridges: A:K.255, A:K.309, B:H.295 Metal complexes: A:H.252, A:H.295 HEC.14: 23 residues within 4Å: Chain B: Y.54, N.55, P.57, D.66, N.67, S.70, R.72, T.73, L.84, A.87, C.88, C.91, K.92, C.172, H.173, Y.176, F.178, V.196, H.241, A.363, H.365 Ligands: SO4.11, HEC.16 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:P.57, B:T.73, B:L.84, B:Y.176, B:Y.176, B:Y.176, B:F.178, B:V.196, B:H.241 Hydrogen bonds: B:N.55, B:N.55, B:A.363 Water bridges: B:Y.54, B:Y.54, B:R.72, B:H.365 Salt bridges: B:R.72, B:H.241, B:H.365 pi-Stacking: B:H.241 HEC.15: 19 residues within 4Å: Chain B: W.11, Y.15, Q.18, F.19, W.22, G.125, C.126, C.129, H.130, L.137, H.161, R.165, V.168, M.264, Y.266, Y.274, S.275, H.277 Ligands: HEC.16 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:W.11, B:Y.15, B:Y.15, B:Q.18, B:F.19, B:W.22, B:L.137, B:V.168 Hydrogen bonds: B:S.275 Salt bridges: B:H.161, B:R.165, B:H.277 Metal complexes: B:H.130, B:H.277 HEC.16: 27 residues within 4Å: Chain B: T.25, Y.28, P.57, R.58, G.59, H.60, Y.62, A.63, D.66, C.91, K.92, I.124, N.128, V.168, C.169, Q.171, C.172, H.173, C.259, H.263, M.264, V.279, K.280, E.281 Ligands: HEC.14, HEC.15, HEC.17 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:K.92, B:Q.171, B:H.263 Hydrogen bonds: B:R.58, B:H.60, B:Y.62 Salt bridges: B:H.60 Metal complexes: B:H.60, B:H.173 HEC.17: 23 residues within 4Å: Chain B: P.57, T.166, C.169, H.173, F.244, W.247, H.252, V.257, S.258, C.259, C.262, H.263, E.281, N.282, P.283, L.284, H.365, G.366, Y.368, F.369, H.370 Ligands: HEC.16, HEC.18 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:T.166, B:H.173, B:W.247, B:L.284, B:F.369, B:F.369 Hydrogen bonds: B:E.281 Water bridges: B:E.281, B:N.282, B:N.282, B:H.365 Metal complexes: B:H.263, B:H.370 HEC.18: 22 residues within 4Å: Chain A: I.251, H.295 Chain B: I.251, H.252, K.255, V.257, C.262, P.283, L.284, S.290, C.291, N.293, C.294, H.295, L.302, I.305, V.306, K.309, F.369, P.372 Ligands: HEC.9, HEC.17 23 PLIP interactions: 19 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:I.251, B:I.251, B:K.255, B:V.257, B:V.257, B:P.283, B:L.284, B:L.302, B:L.302, B:I.305, B:V.306, B:F.369, A:I.251 Water bridges: B:K.255, B:H.295, B:K.309, A:C.294, A:H.295 Salt bridges: B:K.255, B:K.309, A:H.295 Metal complexes: B:H.252, B:H.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Einsle, O. et al., Structure of cytochrome c nitrite reductase. Nature (1999)

Release Date

1999-08-18

Peptides

CYTOCHROME C NITRITE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

CYTOCHROME C NITRITE REDUCTASE

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