SMTL ID : 4n4o.1

Nitrosomonas europea HAO soaked in NH2OH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

hetero-3-3-mer

Ligands

24 x HEC: HEME C(Covalent)

HEC.1: 22 residues within 4Å: Chain A: Y.116, K.117, K.120, C.172, H.176, E.179, R.183, H.204, N.235, C.239, C.242, H.243, A.250, S.253, R.254, R.295, L.296, A.311, M.315, H.323 Ligands: HEC.2, HEC.6 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:E.179, A:E.179, A:R.183, A:A.250, A:R.254, A:L.296, A:A.311 Hydrogen bonds: A:L.296 Water bridges: A:K.297 Salt bridges: A:K.117, A:R.254, A:R.254 Metal complexes: A:H.243, A:H.323 HEC.2: 20 residues within 4Å: Chain A: T.98, H.99, L.102, K.117, K.120, L.121, V.124, L.140, V.143, T.171, C.172, C.175, H.176, C.239, H.243, F.248, S.249, A.250 Ligands: HEC.1, HEC.4 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:T.98, A:L.102, A:L.121, A:V.124, A:L.140, A:V.143, A:F.248, A:F.248 Hydrogen bonds: A:T.98, A:F.248, A:A.250 Water bridges: A:T.98, A:R.254 Salt bridges: A:K.117, A:K.117 Metal complexes: A:H.99, A:H.176 HEC.3: 22 residues within 4Å: Chain A: Y.57, Y.64, P.67, S.69, P.70, A.74, E.75, 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: HEC.4 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain C, Hydrophobic interactions: A:P.67, A:P.70, A:D.78, A:E.86, A:I.146, A:H.149, A:I.164, A:I.164 Hydrogen bonds: A:Y.57, A:Y.64, C:S.365, C:S.365, C:E.366, C:R.367, C:F.368 Metal complexes: A:H.83, A:H.160 Salt bridges: C:R.367 HEC.4: 24 residues within 4Å: Chain A: Y.57, P.60, H.83, W.90, V.91, 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: HEC.2, HEC.3 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:H.83, A:V.91, A:W.94, A:M.166, A:P.167, A:F.248, C:F.368 Water bridges: A:R.245 Salt bridges: A:K.238, A:R.245, A:R.245, C:H.364 pi-Stacking: A:W.90 Metal complexes: A:H.149, A:H.246 Hydrogen bonds: C:S.365 HEC.5: 21 residues within 4Å: Chain A: C.259, H.263, N.270, Y.274, P.308, T.309, C.310, C.313, H.314, T.329, R.330, W.331, A.332, W.356, L.373, M.376, A.458, H.459 Ligands: HEC.6, HEC.7, HEC.12 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:H.263, A:N.270, A:Y.274, A:Y.274, A:Y.274, A:P.308, A:P.308, A:T.329, A:W.356, A:W.356, A:W.356, A:L.373, A:A.458 Hydrogen bonds: A:R.330, A:W.331, A:A.332 Water bridges: A:T.329 Salt bridges: A:H.314, A:R.330, A:H.454 pi-Cation interactions: A:H.314 Metal complexes: A:H.314, A:H.459 HEC.6: 24 residues within 4Å: Chain A: P.202, S.203, H.204, D.207, A.210, C.232, H.233, N.235, N.241, C.242, S.253, A.258, C.259, C.262, H.263, C.310, A.311, H.314, I.325, T.329, A.332 Ligands: HEC.1, HEC.5, HEC.12 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:P.202, A:H.314, A:I.325 Hydrogen bonds: A:P.202, A:S.203, A:D.207 Salt bridges: A:H.233 Metal complexes: A:H.204, A:H.263 HEC.7: 20 residues within 4Å: Chain A: H.279, L.282, F.300, N.306, A.307, P.308, T.359, C.360, C.363, H.364, F.368, Y.372, V.460 Chain E: W.90, M.231, K.238, D.240, T.244, R.245 Ligands: HEC.5 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain E, Hydrophobic interactions: A:F.300, A:P.308, A:P.308, A:Y.372, A:Y.372, A:V.460, E:W.90, E:T.244, E:R.245 Metal complexes: A:H.279, A:H.364 Hydrogen bonds: E:R.245 Water bridges: E:K.238, E:K.238 Salt bridges: E:K.238, E:K.238, E:R.245, E:R.245 HEC.8: 25 residues within 4Å: Chain A: G.463, T.466, Y.467 Chain E: W.197, R.201, A.210, N.211, T.214, W.217, G.228, C.229, C.232, H.233, T.261, C.262, H.263, S.264, H.268, A.332, N.333, Y.334, F.428 Ligands: HEC.27, HEC.28, HOA.31 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain A, Hydrophobic interactions: E:W.197, E:T.214, E:W.217, E:F.428, E:F.428, A:Y.467, A:Y.467 Salt bridges: E:R.201 Metal complexes: E:H.233 HEC.12: 22 residues within 4Å: Chain A: W.197, R.201, A.210, N.211, T.214, W.217, G.228, C.229, C.232, H.233, T.261, C.262, H.263, H.268, N.333, F.428 Chain C: T.466, Y.467 Ligands: HEC.5, HEC.6, HOA.10, 12P.11 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C, Hydrophobic interactions: A:W.197, A:A.210, A:T.214, A:W.217, A:F.428, A:F.428, C:Y.467, C:Y.467 Water bridges: A:N.270 Salt bridges: A:R.201 Metal complexes: A:H.233 HEC.13: 22 residues within 4Å: Chain C: Y.116, K.117, K.120, C.172, H.176, E.179, R.183, H.204, N.235, C.239, C.242, H.243, A.250, S.253, R.254, R.295, L.296, A.311, M.315, H.323 Ligands: HEC.14, HEC.18 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:H.176, C:E.179, C:E.179, C:R.183, C:A.250, C:R.254, C:A.311 Hydrogen bonds: C:L.296 Water bridges: C:K.120, C:K.120, C:K.297 Salt bridges: C:K.117, C:R.254, C:R.254 Metal complexes: C:H.243, C:H.323 HEC.14: 22 residues within 4Å: Chain C: T.98, H.99, L.102, K.117, K.120, L.121, V.124, L.140, V.143, C.148, V.152, T.171, C.172, C.175, H.176, C.239, H.243, F.248, S.249, A.250 Ligands: HEC.13, HEC.16 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:T.98, C:L.102, C:K.120, C:L.121, C:V.124, C:L.140, C:V.143, C:V.143, C:V.152, C:F.248, C:F.248 Hydrogen bonds: C:F.248, C:A.250 Water bridges: C:T.98, C:T.98, C:A.251, C:R.254 Salt bridges: C:K.117, C:K.117 Metal complexes: C:H.99, C:H.176 HEC.15: 21 residues within 4Å: Chain C: Y.57, Y.64, P.67, P.70, E.72, A.74, C.79, C.82, H.83, E.86, C.145, I.146, H.149, V.150, H.160, I.164, M.166 Chain E: S.365, E.366, R.367 Ligands: HEC.16 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain E, Hydrophobic interactions: C:P.67, C:E.72, C:A.74, C:E.86, C:H.149, C:V.150, C:I.164, C:I.164 Hydrogen bonds: C:Y.57, C:Y.64, E:S.365, E:E.366, E:R.367 Metal complexes: C:H.83, C:H.160 Salt bridges: E:R.367 HEC.16: 24 residues within 4Å: Chain C: Y.57, P.60, H.83, T.87, 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 E: H.364, S.365, F.368 Ligands: HEC.14, HEC.15 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain E, Hydrophobic interactions: C:H.83, C:W.94, C:M.166, C:P.167, C:F.248 Water bridges: C:R.245 Salt bridges: C:K.238, C:R.245, C:R.245, E:H.364 pi-Stacking: C:W.90 Metal complexes: C:H.149, C:H.246 Hydrogen bonds: E:S.365 HEC.17: 21 residues within 4Å: Chain C: C.259, H.263, N.270, Y.274, P.308, T.309, C.310, C.313, H.314, T.329, R.330, W.331, A.332, W.356, L.373, M.376, A.458, H.459 Ligands: HEC.18, HEC.19, HEC.22 20 PLIP interactions: 20 interactions with chain C, Hydrophobic interactions: C:H.263, C:N.270, C:Y.274, C:Y.274, C:Y.274, C:Y.274, C:P.308, C:P.308, C:T.329, C:W.356, C:W.356, C:W.356, C:L.373, C:A.458 Hydrogen bonds: C:R.330, C:W.331, C:A.332 Salt bridges: C:R.330 Metal complexes: C:H.314, C:H.459 HEC.18: 23 residues within 4Å: Chain C: P.202, S.203, H.204, D.207, A.210, C.232, H.233, N.235, N.241, C.242, S.253, A.258, C.259, C.262, H.263, C.310, H.314, I.325, T.329, A.332 Ligands: HEC.13, HEC.17, HEC.22 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:I.325, C:I.325 Hydrogen bonds: C:P.202, C:S.203 Salt bridges: C:H.233 Metal complexes: C:H.204, C:H.263 HEC.19: 22 residues within 4Å: Chain A: W.90, M.231, K.238, D.240, T.244, R.245 Chain C: K.278, H.279, L.282, F.300, N.306, A.307, P.308, T.359, C.360, C.363, H.364, F.368, Y.372, L.373, V.460 Ligands: HEC.17 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain A, Hydrophobic interactions: C:F.300, C:P.308, C:Y.372, C:Y.372, C:L.373, C:V.460, A:W.90, A:R.245 Metal complexes: C:H.279, C:H.364 Hydrogen bonds: A:R.245 Water bridges: A:K.238, A:R.245 Salt bridges: A:K.238, A:K.238, A:R.245, A:R.245 HEC.22: 24 residues within 4Å: Chain C: W.197, R.201, A.210, N.211, T.214, W.217, G.228, C.229, C.232, H.233, T.261, C.262, H.263, H.268, N.333, Y.334, F.428 Chain E: G.463, T.466, Y.467 Ligands: HEC.17, HEC.18, HOA.20, 12P.21 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain E, Hydrophobic interactions: C:W.197, C:A.210, C:T.214, C:W.217, C:F.428, E:Y.467, E:Y.467 Water bridges: C:H.268, C:N.270, C:N.270 Salt bridges: C:R.201 Metal complexes: C:H.233 HEC.23: 22 residues within 4Å: Chain E: Y.116, K.117, K.120, C.172, H.176, E.179, R.183, H.204, N.235, C.239, C.242, H.243, A.250, S.253, R.254, R.295, L.296, A.311, M.315, H.323 Ligands: HEC.24, HEC.28 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:E.179, E:R.183, E:A.250, E:R.254, E:A.311 Hydrogen bonds: E:L.296 Water bridges: E:R.254, E:R.254, E:K.297 Salt bridges: E:K.117, E:R.254, E:R.254 Metal complexes: E:H.243, E:H.323 HEC.24: 22 residues within 4Å: Chain E: T.98, H.99, L.102, K.117, K.120, L.121, V.124, L.140, V.143, C.148, V.152, T.171, C.172, C.175, H.176, C.239, H.243, F.248, S.249, A.250 Ligands: HEC.23, HEC.26 22 PLIP interactions: 22 interactions with chain E, Hydrophobic interactions: E:T.98, E:L.102, E:K.120, E:L.121, E:V.124, E:L.140, E:V.143, E:V.152, E:F.248, E:F.248 Hydrogen bonds: E:T.98, E:K.117, E:F.248, E:A.250 Water bridges: E:T.98, E:A.251, E:R.254 Salt bridges: E:K.117, E:K.117, E:H.176 Metal complexes: E:H.99, E:H.176 HEC.25: 21 residues within 4Å: Chain A: S.365, E.366, R.367 Chain E: Y.57, Y.64, P.67, S.69, P.70, E.72, A.74, C.79, C.82, H.83, E.86, C.145, I.146, H.149, H.160, I.164, M.166 Ligands: HEC.26 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain A, Hydrophobic interactions: E:P.70, E:E.72, E:E.86, E:H.149, E:I.164 Hydrogen bonds: E:Y.57, E:Y.64, A:S.365, A:E.366, A:R.367 Metal complexes: E:H.83, E:H.160 Salt bridges: A:R.367 HEC.26: 24 residues within 4Å: Chain A: H.364, S.365, F.368 Chain E: Y.57, P.60, H.83, T.87, 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: HEC.24, HEC.25 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain A, Hydrophobic interactions: E:H.83, E:W.94, E:D.240, E:F.248, A:F.368 Water bridges: E:R.245 Salt bridges: E:K.238, E:R.245, E:R.245, A:H.364 pi-Stacking: E:W.90 Metal complexes: E:H.149, E:H.246 Hydrogen bonds: A:S.365 HEC.27: 21 residues within 4Å: Chain E: C.259, H.263, N.270, Y.274, H.279, P.308, T.309, C.310, C.313, H.314, T.329, R.330, W.331, A.332, W.356, M.376, A.458, H.459 Ligands: HEC.8, HEC.28, HEC.29 21 PLIP interactions: 21 interactions with chain E, Hydrophobic interactions: E:H.263, E:N.270, E:Y.274, E:Y.274, E:Y.274, E:Y.274, E:P.308, E:P.308, E:T.329, E:W.356, E:W.356, E:W.356, E:A.458 Hydrogen bonds: E:R.330, E:W.331, E:A.332 Salt bridges: E:H.314, E:R.330, E:H.454 Metal complexes: E:H.314, E:H.459 HEC.28: 24 residues within 4Å: Chain E: P.202, S.203, H.204, D.207, A.210, C.232, H.233, N.235, N.241, C.242, S.253, A.258, C.259, C.262, H.263, C.310, A.311, H.314, I.325, T.329, A.332 Ligands: HEC.8, HEC.23, HEC.27 10 PLIP interactions: 10 interactions with chain E, Hydrophobic interactions: E:P.202, E:D.207, E:H.314, E:I.325, E:I.325 Hydrogen bonds: E:P.202, E:S.203 Salt bridges: E:H.233 Metal complexes: E:H.204, E:H.263 HEC.29: 21 residues within 4Å: Chain C: W.90, M.231, K.238, D.240, T.244, R.245 Chain E: K.278, H.279, L.282, F.300, N.306, A.307, P.308, T.359, C.360, C.363, H.364, F.368, Y.372, V.460 Ligands: HEC.27 19 PLIP interactions: 10 interactions with chain E, 9 interactions with chain C, Hydrophobic interactions: E:F.300, E:P.308, E:P.308, E:F.368, E:F.368, E:Y.372, E:Y.372, E:V.460, C:W.90, C:R.245 Metal complexes: E:H.279, E:H.364 Hydrogen bonds: C:R.245 Water bridges: C:K.238, C:K.238 Salt bridges: C:K.238, C:K.238, C:R.245, C:R.245

1 x K: POTASSIUM ION(Non-covalent)

K.9: 3 residues within 4Å: Chain A: D.288 Chain C: D.288 Chain E: D.288 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:D.288, C:D.288, E:D.288, A:D.288, H2O.7

3 x HOA: HYDROXYAMINE(Non-covalent)

HOA.10: 5 residues within 4Å: Chain A: D.267, H.268, Y.334 Chain C: Y.467 Ligands: HEC.12 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.467, A:H.268, A:Y.334 HOA.20: 5 residues within 4Å: Chain C: D.267, H.268, Y.334 Chain E: Y.467 Ligands: HEC.22 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:H.268, C:Y.334, E:Y.467 HOA.31: 5 residues within 4Å: Chain A: Y.467 Chain E: D.267, H.268, Y.334 Ligands: HEC.8 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:Y.467, E:H.268, E:Y.334

2 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.11: 6 residues within 4Å: Chain A: Y.334, F.336, V.337, F.424, E.447 Ligands: HEC.12 No protein-ligand interaction detected (PLIP) 12P.21: 11 residues within 4Å: Chain C: Q.196, W.197, P.198, Y.334, F.336, Y.387, G.422, F.424, L.443, E.447 Ligands: HEC.22 1 PLIP interactions: 1 interactions with chain C Water bridges: C:F.424

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.30: 5 residues within 4Å: Chain E: L.15, D.16, K.19, A.20, E.24 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.16, E:D.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maalcke, W.J. et al., Structural Basis of Biological NO Generation by Octaheme Oxidoreductases. J.Biol.Chem. (2014)

Release Date

2013-12-11

Peptides

Hydroxylamine oxidoreductase: ACE
hydroxylamine oxidoreductase: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Hydroxylamine oxidoreductase

hydroxylamine oxidoreductase

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