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

X-RAY STRUCTURE OF HYDROXYLAMINE OXIDOREDUCTASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

21 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 20 residues within 4Å: Chain A: Y.57, Y.64, P.67, P.70, A.74, D.78, C.79, C.82, H.83, E.86, C.145, I.146, H.149, H.160, I.164, M.166 Chain B: S.365, E.366, R.367 Ligands: HEM.2 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:P.67, A:P.70, A:A.74, A:D.78, A:H.149, A:I.164, A:I.164 Hydrogen bonds: A:Y.64, A:Y.64, B:S.365, B:E.366, B:E.366, B:E.366, B:R.367 Metal complexes: A:H.83, A:H.160 Salt bridges: B:R.367 HEM.2: 23 residues within 4Å: Chain A: Y.57, P.60, H.83, W.90, W.94, H.99, V.143, G.144, C.145, C.148, H.149, M.166, P.167, K.238, D.240, R.245, H.246, F.248 Chain B: H.364, S.365, F.368 Ligands: HEM.1, HEM.3 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain A, Hydrophobic interactions: B:F.368, A:H.83, A:M.166, A:P.167, A:F.248, A:F.248 Hydrogen bonds: B:S.365 Salt bridges: B:H.364, A:K.238, A:R.245, A:R.245 pi-Stacking: A:W.90 Metal complexes: A:H.149, A:H.246 HEM.3: 21 residues within 4Å: Chain A: T.98, H.99, L.102, K.117, K.120, L.121, V.124, L.140, V.143, V.152, T.171, C.172, C.175, H.176, C.239, H.243, F.248, S.249, A.250 Ligands: HEM.2, HEM.5 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:T.98, A:L.121, A:V.124, A:L.140, A:V.143, A:V.152, A:F.248, A:F.248, A:F.248 Hydrogen bonds: A:A.250 Salt bridges: A:K.117, A:K.117 Metal complexes: A:H.99, A:H.176 HEM.5: 20 residues within 4Å: Chain A: Y.116, K.117, K.120, C.172, H.176, E.179, H.204, N.235, C.239, C.242, H.243, A.250, S.253, R.254, R.295, L.296, M.315, H.323 Ligands: HEM.3, HEM.6 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:E.179, A:A.250, A:R.254 Hydrogen bonds: A:Y.116, A:L.296 Salt bridges: A:K.117, A:R.254, A:R.254 pi-Stacking: A:H.243, A:H.323 Metal complexes: A:H.243, A:H.323 HEM.6: 21 residues within 4Å: Chain A: R.201, P.202, S.203, H.204, A.210, C.232, H.233, N.235, N.241, C.242, A.258, C.259, C.262, H.263, C.310, H.314, T.329, A.332 Ligands: HEC.4, HEM.5, HEM.7 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:N.241 Hydrogen bonds: A:S.203 Salt bridges: A:H.233 Metal complexes: A:H.204, A:H.263 HEM.7: 21 residues within 4Å: Chain A: C.259, H.263, N.270, W.271, Y.274, H.279, P.308, T.309, C.310, C.313, H.314, T.329, R.330, W.331, W.356, M.376, A.458, H.459 Ligands: HEC.4, HEM.6, HEM.8 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:H.263, A:N.270, A:W.271, A:Y.274, A:Y.274, A:T.329, A:W.356, A:W.356, A:W.356, A:A.458 Hydrogen bonds: A:R.330, A:W.331 Salt bridges: A:H.314, A:R.330, A:H.454 Metal complexes: A:H.314, A:H.459 HEM.8: 19 residues within 4Å: Chain A: K.278, H.279, L.282, N.306, A.307, P.308, T.359, C.360, C.363, H.364, F.368, Y.372, V.460 Chain C: M.231, K.238, D.240, T.244, R.245 Ligands: HEM.7 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain A, Hydrogen bonds: C:R.245 Salt bridges: C:K.238, C:K.238, C:R.245, C:R.245 Hydrophobic interactions: A:L.282, A:F.368, A:F.368, A:Y.372, A:Y.372, A:V.460 Metal complexes: A:H.279, A:H.364 HEM.9: 20 residues within 4Å: Chain B: Y.57, Y.64, P.67, P.70, A.74, D.78, C.79, C.82, H.83, E.86, C.145, I.146, H.149, H.160, I.164, M.166 Chain C: S.365, E.366, R.367 Ligands: HEM.10 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain C, Hydrophobic interactions: B:P.67, B:P.70, B:A.74, B:D.78, B:H.149, B:I.164, B:I.164 Hydrogen bonds: B:Y.64, B:Y.64, C:S.365, C:E.366, C:E.366, C:E.366, C:R.367 Metal complexes: B:H.83, B:H.160 Salt bridges: C:R.367 HEM.10: 23 residues within 4Å: Chain B: Y.57, P.60, H.83, W.90, W.94, H.99, V.143, G.144, C.145, C.148, H.149, M.166, P.167, K.238, D.240, R.245, H.246, F.248 Chain C: H.364, S.365, F.368 Ligands: HEM.9, HEM.11 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain C, Hydrophobic interactions: B:H.83, B:M.166, B:P.167, B:F.248, B:F.248, C:F.368 Salt bridges: B:K.238, B:R.245, B:R.245, C:H.364 pi-Stacking: B:W.90 Metal complexes: B:H.149, B:H.246 Hydrogen bonds: C:S.365 HEM.11: 21 residues within 4Å: Chain B: T.98, H.99, L.102, K.117, K.120, L.121, V.124, L.140, V.143, V.152, T.171, C.172, C.175, H.176, C.239, H.243, F.248, S.249, A.250 Ligands: HEM.10, HEM.13 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:T.98, B:L.121, B:V.124, B:L.140, B:V.143, B:V.152, B:F.248, B:F.248, B:F.248 Hydrogen bonds: B:A.250 Salt bridges: B:K.117, B:K.117 Metal complexes: B:H.99, B:H.176 HEM.13: 20 residues within 4Å: Chain B: Y.116, K.117, K.120, C.172, H.176, E.179, H.204, N.235, C.239, C.242, H.243, A.250, S.253, R.254, R.295, L.296, M.315, H.323 Ligands: HEM.11, HEM.14 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:E.179, B:A.250, B:R.254 Hydrogen bonds: B:Y.116, B:L.296 Salt bridges: B:K.117, B:R.254, B:R.254 pi-Stacking: B:H.243, B:H.323 Metal complexes: B:H.243, B:H.323 HEM.14: 21 residues within 4Å: Chain B: R.201, P.202, S.203, H.204, A.210, C.232, H.233, N.235, N.241, C.242, A.258, C.259, C.262, H.263, C.310, H.314, T.329, A.332 Ligands: HEC.12, HEM.13, HEM.15 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:N.241 Hydrogen bonds: B:S.203 Salt bridges: B:H.233 Metal complexes: B:H.204, B:H.263 HEM.15: 21 residues within 4Å: Chain B: C.259, H.263, N.270, W.271, Y.274, H.279, P.308, T.309, C.310, C.313, H.314, T.329, R.330, W.331, W.356, M.376, A.458, H.459 Ligands: HEC.12, HEM.14, HEM.16 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:H.263, B:N.270, B:W.271, B:Y.274, B:Y.274, B:T.329, B:W.356, B:W.356, B:W.356, B:A.458 Hydrogen bonds: B:R.330, B:W.331 Salt bridges: B:H.314, B:R.330, B:H.454 Metal complexes: B:H.314, B:H.459 HEM.16: 19 residues within 4Å: Chain A: M.231, K.238, D.240, T.244, R.245 Chain B: K.278, H.279, L.282, N.306, A.307, P.308, T.359, C.360, C.363, H.364, F.368, Y.372, V.460 Ligands: HEM.15 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B, Hydrogen bonds: A:R.245 Salt bridges: A:K.238, A:K.238, A:R.245, A:R.245 Hydrophobic interactions: B:L.282, B:F.368, B:F.368, B:Y.372, B:Y.372, B:V.460 Metal complexes: B:H.279, B:H.364 HEM.17: 20 residues within 4Å: Chain A: S.365, E.366, R.367 Chain C: Y.57, Y.64, P.67, P.70, A.74, D.78, C.79, C.82, H.83, E.86, C.145, I.146, H.149, H.160, I.164, M.166 Ligands: HEM.18 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain A, Hydrophobic interactions: C:P.67, C:P.70, C:A.74, C:D.78, C:H.149, C:I.164, C:I.164 Hydrogen bonds: C:Y.64, C:Y.64, A:S.365, A:E.366, A:E.366, A:E.366, A:R.367 Metal complexes: C:H.83, C:H.160 Salt bridges: A:R.367 HEM.18: 23 residues within 4Å: Chain A: H.364, S.365, F.368 Chain C: Y.57, P.60, H.83, W.90, W.94, H.99, V.143, G.144, C.145, C.148, H.149, M.166, P.167, K.238, D.240, R.245, H.246, F.248 Ligands: HEM.17, HEM.19 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain A, Hydrophobic interactions: C:H.83, C:M.166, C:P.167, C:F.248, C:F.248, A:F.368 Salt bridges: C:K.238, C:R.245, C:R.245, A:H.364 pi-Stacking: C:W.90 Metal complexes: C:H.149, C:H.246 Hydrogen bonds: A:S.365 HEM.19: 21 residues within 4Å: Chain C: T.98, H.99, L.102, K.117, K.120, L.121, V.124, L.140, V.143, V.152, T.171, C.172, C.175, H.176, C.239, H.243, F.248, S.249, A.250 Ligands: HEM.18, HEM.21 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:T.98, C:L.121, C:V.124, C:L.140, C:V.143, C:V.152, C:F.248, C:F.248, C:F.248 Hydrogen bonds: C:A.250 Salt bridges: C:K.117, C:K.117 Metal complexes: C:H.99, C:H.176 HEM.21: 20 residues within 4Å: Chain C: Y.116, K.117, K.120, C.172, H.176, E.179, H.204, N.235, C.239, C.242, H.243, A.250, S.253, R.254, R.295, L.296, M.315, H.323 Ligands: HEM.19, HEM.22 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:E.179, C:A.250, C:R.254 Hydrogen bonds: C:Y.116, C:L.296 Salt bridges: C:K.117, C:R.254, C:R.254 pi-Stacking: C:H.243, C:H.323 Metal complexes: C:H.243, C:H.323 HEM.22: 21 residues within 4Å: Chain C: R.201, P.202, S.203, H.204, A.210, C.232, H.233, N.235, N.241, C.242, A.258, C.259, C.262, H.263, C.310, H.314, T.329, A.332 Ligands: HEC.20, HEM.21, HEM.23 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:N.241 Hydrogen bonds: C:S.203 Salt bridges: C:H.233 Metal complexes: C:H.204, C:H.263 HEM.23: 21 residues within 4Å: Chain C: C.259, H.263, N.270, W.271, Y.274, H.279, P.308, T.309, C.310, C.313, H.314, T.329, R.330, W.331, W.356, M.376, A.458, H.459 Ligands: HEC.20, HEM.22, HEM.24 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:H.263, C:N.270, C:W.271, C:Y.274, C:Y.274, C:T.329, C:W.356, C:W.356, C:W.356, C:A.458 Hydrogen bonds: C:R.330, C:W.331 Salt bridges: C:H.314, C:R.330, C:H.454 Metal complexes: C:H.314, C:H.459 HEM.24: 19 residues within 4Å: Chain B: M.231, K.238, D.240, T.244, R.245 Chain C: K.278, H.279, L.282, N.306, A.307, P.308, T.359, C.360, C.363, H.364, F.368, Y.372, V.460 Ligands: HEM.23 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain B, Hydrophobic interactions: C:L.282, C:F.368, C:F.368, C:Y.372, C:Y.372, C:V.460 Metal complexes: C:H.279, C:H.364 Hydrogen bonds: B:R.245 Salt bridges: B:K.238, B:K.238, B:R.245, B:R.245

3 x HEC: HEME C(Covalent)

HEC.4: 23 residues within 4Å: Chain A: W.197, R.201, P.202, A.210, N.211, T.214, W.217, M.220, G.228, C.229, C.232, H.233, T.261, C.262, H.263, H.268, A.332, N.333, F.428 Chain B: T.466, Y.467 Ligands: HEM.6, HEM.7 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:W.197, A:T.214, A:W.217, A:F.428, B:Y.467, B:Y.467 Salt bridges: A:R.201 Metal complexes: A:H.233 HEC.12: 23 residues within 4Å: Chain B: W.197, R.201, P.202, A.210, N.211, T.214, W.217, M.220, G.228, C.229, C.232, H.233, T.261, C.262, H.263, H.268, A.332, N.333, F.428 Chain C: T.466, Y.467 Ligands: HEM.14, HEM.15 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:W.197, B:T.214, B:W.217, B:F.428, C:Y.467, C:Y.467 Salt bridges: B:R.201 Metal complexes: B:H.233 HEC.20: 23 residues within 4Å: Chain A: T.466, Y.467 Chain C: W.197, R.201, P.202, A.210, N.211, T.214, W.217, M.220, G.228, C.229, C.232, H.233, T.261, C.262, H.263, H.268, A.332, N.333, F.428 Ligands: HEM.22, HEM.23 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A, Hydrophobic interactions: C:W.197, C:T.214, C:W.217, C:F.428, A:Y.467, A:Y.467 Salt bridges: C:R.201 Metal complexes: C:H.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Igarashi, N. et al., The 2.8 A structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea. Nat.Struct.Biol. (1997)

Release Date

1998-03-04

Peptides

HYDROXYLAMINE OXIDOREDUCTASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

HYDROXYLAMINE OXIDOREDUCTASE

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