SMTL ID : 3tor.2 (1 other biounit)

Crystal structure of Escherichia coli NrfA with Europium bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.189, Y.190, Y.216, K.235, Q.237 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.189, A:Y.190, A:K.235, H2O.4, H2O.7 CA.10: 5 residues within 4Å: Chain B: E.189, Y.190, Y.216, K.235, Q.237 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.189, B:Y.190, B:K.235, H2O.22, H2O.25

5 x EU: EUROPIUM ION(Non-covalent)(Non-functional Binders)

EU.2: 3 residues within 4Å: Chain A: P.65 Ligands: HEC.5, HEC.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:P.65, H2O.3, H2O.4, H2O.7, H2O.8 EU.8: 2 residues within 4Å: Ligands: HEC.7, HEC.16 No protein-ligand interaction detected (PLIP) EU.9: 2 residues within 4Å: Ligands: HEC.7, HEC.16 No protein-ligand interaction detected (PLIP) EU.11: 3 residues within 4Å: Chain B: P.65 Ligands: HEC.14, HEC.15 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:P.65, H2O.27, H2O.29, H2O.34, H2O.35 EU.17: 1 residues within 4Å: Chain B: E.164 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.164, B:E.164, H2O.23, H2O.27, H2O.29

10 x HEC: HEME C(Covalent)(Non-covalent)

HEC.3: 23 residues within 4Å: Chain A: Y.62, N.63, P.65, D.74, V.75, T.78, R.80, T.81, L.92, A.95, C.96, C.99, K.100, C.186, H.187, V.188, Y.190, F.192, V.199, H.238, A.360, H.362 Ligands: HEC.5 23 PLIP interactions: 22 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:P.65, A:P.65, A:V.75, A:T.78, A:T.81, A:L.92, A:V.188, A:Y.190, A:Y.190, A:Y.190, A:F.192, A:V.199, A:H.238 Hydrogen bonds: A:N.63, A:N.63 Water bridges: A:R.80, A:E.240, A:H.362 Salt bridges: A:R.80, A:H.238, A:H.362 pi-Stacking: A:H.238 Metal complexes: H2O.9 HEC.4: 24 residues within 4Å: Chain A: F.19, H.23, Q.26, Y.27, W.30, L.132, G.133, C.134, C.137, H.138, F.145, G.148, P.150, L.152, R.175, Q.179, I.257, M.261, K.263, Y.272, T.273, H.275, I.277 Ligands: HEC.5 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:F.19, A:H.23, A:Q.26, A:Q.26, A:Y.27, A:W.30, A:L.132, A:F.145, A:L.152, A:L.152, A:I.257, A:I.277 Hydrogen bonds: A:Q.179, A:T.273 Water bridges: A:R.175, A:R.175, A:K.263 Salt bridges: A:R.175, A:K.263, A:K.263 Metal complexes: A:H.138, A:H.275 HEC.5: 28 residues within 4Å: Chain A: Q.36, P.65, R.66, G.67, H.68, F.70, A.71, D.74, C.99, K.100, L.132, D.136, C.137, R.156, V.182, C.183, C.186, H.187, C.256, I.257, H.260, M.261, I.277, G.278 Ligands: EU.2, HEC.3, HEC.4, HEC.6 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:P.65, A:A.71, A:K.100, A:L.132, A:L.132, A:I.257, A:H.260, A:I.277 Hydrogen bonds: A:Q.36, A:R.66, A:F.70 Metal complexes: A:H.68, A:H.187 HEC.6: 24 residues within 4Å: Chain A: P.65, C.183, H.187, E.240, Y.241, W.244, H.249, V.254, T.255, C.256, C.259, H.260, N.279, P.280, F.281, V.303, H.362, G.363, H.365, M.366, H.367 Ligands: EU.2, HEC.5, HEC.7 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:H.187, A:E.240, A:E.240, A:W.244, A:W.244, A:H.249, A:V.254, A:P.280, A:F.281, A:H.362 Hydrogen bonds: A:N.279 Water bridges: A:H.362 Salt bridges: A:H.365 Metal complexes: A:H.260, A:H.367 HEC.7: 23 residues within 4Å: Chain A: I.248, H.249, N.252, V.254, D.258, C.259, P.280, F.281, T.287, C.288, C.291, H.292, V.302, V.303, R.306, M.366 Chain B: I.248, H.292, Q.294 Ligands: HEC.6, EU.8, EU.9, HEC.16 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:I.248, A:N.252, A:V.254, A:P.280, A:F.281, A:V.302, A:V.303 Water bridges: A:I.248, A:I.248, A:R.306, B:H.292 Salt bridges: A:R.306, B:H.292 Metal complexes: A:H.249, A:H.292 Hydrogen bonds: B:Q.294 HEC.12: 25 residues within 4Å: Chain B: Y.62, N.63, P.65, D.74, V.75, T.78, R.80, T.81, L.92, A.95, C.96, C.99, K.100, Q.185, C.186, H.187, V.188, Y.190, F.192, V.199, F.201, H.238, A.360, H.362 Ligands: HEC.14 25 PLIP interactions: 24 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:P.65, B:P.65, B:V.75, B:T.78, B:T.81, B:L.92, B:V.188, B:Y.190, B:Y.190, B:Y.190, B:F.192, B:V.199, B:F.201, B:H.238 Hydrogen bonds: B:N.63, B:N.63, B:A.360 Water bridges: B:Y.62, B:Y.62, B:R.80 Salt bridges: B:R.80, B:H.238, B:H.362 pi-Stacking: B:H.238 Metal complexes: H2O.30 HEC.13: 24 residues within 4Å: Chain B: F.19, H.23, Q.26, Y.27, W.30, L.132, G.133, C.134, C.137, H.138, F.145, G.148, P.150, L.152, R.175, Q.179, I.257, M.261, K.263, Y.272, T.273, H.275, I.277 Ligands: HEC.14 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.19, B:H.23, B:Q.26, B:Y.27, B:W.30, B:L.132, B:F.145, B:F.145, B:L.152, B:I.257, B:I.277 Hydrogen bonds: B:Q.179, B:T.273 Water bridges: B:R.175, B:K.263, B:T.273 Salt bridges: B:R.175, B:K.263, B:K.263 Metal complexes: B:H.138, B:H.275 HEC.14: 27 residues within 4Å: Chain B: Q.36, P.65, R.66, G.67, H.68, F.70, A.71, D.74, C.99, K.100, L.132, D.136, C.137, R.156, V.182, C.183, C.186, H.187, C.256, I.257, H.260, M.261, I.277 Ligands: EU.11, HEC.12, HEC.13, HEC.15 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:P.65, B:A.71, B:K.100, B:L.132, B:L.132, B:I.257, B:H.260, B:I.277, B:I.277 Hydrogen bonds: B:Q.36, B:F.70, B:D.74 Water bridges: B:N.279 Metal complexes: B:H.68, B:H.187 HEC.15: 24 residues within 4Å: Chain B: P.65, C.183, H.187, E.240, Y.241, W.244, H.249, V.254, T.255, C.256, C.259, H.260, N.279, P.280, F.281, V.303, H.362, G.363, H.365, M.366, H.367 Ligands: EU.11, HEC.14, HEC.16 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:H.187, B:E.240, B:W.244, B:W.244, B:H.249, B:V.254, B:P.280, B:F.281, B:H.362 Hydrogen bonds: B:N.279 Water bridges: B:H.362 Salt bridges: B:K.307, B:H.365 Metal complexes: B:H.260, B:H.367 HEC.16: 22 residues within 4Å: Chain A: I.248, H.292, Q.294 Chain B: I.248, H.249, N.252, V.254, D.258, C.259, P.280, F.281, T.287, C.288, C.291, H.292, V.302, R.306, M.366 Ligands: HEC.7, EU.8, EU.9, HEC.15 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:I.248, B:N.252, B:V.254, B:P.280, B:F.281, B:V.302 Water bridges: B:R.306 Salt bridges: B:R.306, A:H.292 Metal complexes: B:H.249, B:H.292 Hydrogen bonds: A:Q.294

Links

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Citation

Lockwood, C.W. et al., Characterization of the active site and calcium binding in cytochrome c nitrite reductases. Biochem.Soc.Trans. (2011)

Release Date

2011-12-07

Peptides

Cytochrome c nitrite reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Cytochrome c nitrite reductase

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