SMTL ID : 1gu6.2 (1 other biounit)

Structure of the Periplasmic Cytochrome c Nitrite Reductase from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

4 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.189, A:E.189, A:Y.190, A:K.235, H2O.3 CA.2: 3 residues within 4Å: Chain A: P.65 Ligands: HEC.6, HEC.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.65, H2O.5 CA.9: 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.9, H2O.9 CA.10: 3 residues within 4Å: Chain B: P.65 Ligands: HEC.14, HEC.15 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:P.65, H2O.12

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: M.207, K.208, V.209, E.242, T.243, A.246, E.371, R.374, M.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.209, A:E.242, A:T.243, A:R.374 GOL.11: 9 residues within 4Å: Chain B: M.207, K.208, V.209, E.242, T.243, A.246, E.371, R.374, M.375 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.209, B:E.242, B:T.245, B:E.371, B:R.374 Water bridges: B:K.208

10 x HEC: HEME C(Covalent)

HEC.4: 21 residues within 4Å: Chain A: Y.62, N.63, P.65, D.74, T.78, R.80, T.81, L.92, A.95, C.96, C.99, K.100, C.186, H.187, Y.190, F.192, V.199, H.238, A.360, H.362 Ligands: HEC.6 19 PLIP interactions: 18 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:P.65, A:T.78, A:T.81, A:L.92, 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, A:A.360 Water bridges: A:Y.62, A:Y.62 Salt bridges: A:R.80, A:H.238, A:H.362 Metal complexes: H2O.5 HEC.5: 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.6 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:F.19, A:H.23, A:Q.26, A:Y.27, A:W.30, A:L.132, A:F.145, A:P.150, A:L.152, A:L.152, A:I.257, A:I.277 Hydrogen bonds: A:Q.179, A:T.273 Salt bridges: A:R.175, A:K.263, A:K.263 pi-Stacking: A:H.138, A:H.138, A:H.275, A:H.275 Metal complexes: A:H.138, A:H.275 HEC.6: 24 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, V.182, C.183, C.186, H.187, C.256, H.260, M.261, I.277, G.278 Ligands: CA.2, HEC.4, HEC.5, HEC.7 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:P.65, A:A.71, A:K.100, A:L.132, A:H.260, A:I.277, A:I.277 Hydrogen bonds: A:Q.36, A:R.66, A:F.70, A:D.74 pi-Stacking: A:H.68, A:H.68, A:H.68, A:H.187, A:H.187 Metal complexes: A:H.68, A:H.187 HEC.7: 22 residues within 4Å: Chain A: P.65, C.183, H.187, E.240, W.244, H.249, V.254, T.255, C.256, C.259, H.260, N.279, P.280, F.281, V.303, H.362, H.365, M.366, H.367 Ligands: CA.2, HEC.6, HEC.8 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:H.187, A:W.244, A:H.249, A:V.254, A:F.281 Hydrogen bonds: A:N.279 Salt bridges: A:H.365 pi-Stacking: A:H.260, A:H.260, A:H.260, A:H.367, A:H.367 pi-Cation interactions: A:H.260 Metal complexes: A:H.260, A:H.367 HEC.8: 17 residues within 4Å: Chain A: I.248, H.249, V.254, D.258, P.280, F.281, T.287, C.288, C.291, H.292, L.299, R.306, M.366 Chain B: H.292, Q.294 Ligands: HEC.7, HEC.16 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:I.248, A:P.280, A:F.281, A:L.299 Water bridges: A:I.248 Salt bridges: A:R.306, B:H.292 pi-Stacking: A:H.249, A:H.249, A:H.292, A:H.292 Metal complexes: A:H.249, A:H.292 Hydrogen bonds: B:Q.294 HEC.12: 20 residues within 4Å: Chain B: Y.62, N.63, P.65, D.74, T.78, R.80, T.81, L.92, A.95, C.96, C.99, K.100, C.186, H.187, Y.190, F.192, V.199, H.238, H.362 Ligands: HEC.14 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:P.65, B:T.78, B:T.81, B:L.92, B:Y.190, B:Y.190, B:Y.190, B:F.192, B:V.199, B:H.238 Hydrogen bonds: B:N.63, B:N.63, B:A.360 Water bridges: B:H.362 Salt bridges: B:R.80, B:H.238, B:H.362 pi-Stacking: B:H.238 pi-Cation interactions: B:K.100 Metal complexes: H2O.12 HEC.13: 23 residues within 4Å: Chain B: F.19, H.23, Q.26, Y.27, W.30, 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 24 PLIP interactions: 24 interactions with chain B, Hydrophobic interactions: B:F.19, B:H.23, B:Q.26, B:Y.27, B:W.30, B:F.145, B:P.150, B:L.152, B:L.152, B:I.257, B:I.277 Hydrogen bonds: B:Q.179, B:T.273 Water bridges: B:R.175, B:R.175 Salt bridges: B:R.175, B:K.263, B:K.263 pi-Stacking: B:H.138, B:H.138, B:H.275, B:H.275 Metal complexes: B:H.138, B:H.275 HEC.14: 23 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, V.182, C.183, C.186, H.187, H.260, M.261, I.277, G.278 Ligands: CA.10, HEC.12, HEC.13, HEC.15 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:P.65, B:A.71, B:K.100, B:L.132, B:H.260, B:I.277, B:I.277 Hydrogen bonds: B:Q.36, B:R.66, B:F.70, B:D.74 pi-Stacking: B:H.68, B:H.68, B:H.187, B:H.187 Metal complexes: B:H.68, B:H.187 HEC.15: 21 residues within 4Å: Chain B: C.183, H.187, E.240, W.244, H.249, V.254, T.255, C.256, C.259, H.260, N.279, P.280, F.281, V.303, H.362, H.365, M.366, H.367 Ligands: CA.10, HEC.14, HEC.16 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:H.187, B:W.244, B:V.254, B:F.281 Hydrogen bonds: B:N.279 Salt bridges: B:H.365 pi-Stacking: B:H.260, B:H.260, B:H.260, B:H.367, B:H.367 pi-Cation interactions: B:H.260 Metal complexes: B:H.260, B:H.367 HEC.16: 17 residues within 4Å: Chain A: H.292, Q.294 Chain B: I.248, H.249, V.254, D.258, P.280, F.281, T.287, C.288, C.291, H.292, L.299, R.306, M.366 Ligands: HEC.8, HEC.15 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:I.248, B:V.254, B:V.254, B:P.280, B:F.281, B:L.299 Water bridges: B:I.248, B:R.306 Salt bridges: B:R.306, A:H.292 pi-Stacking: B:H.249, B:H.249, B:H.292, B:H.292 Metal complexes: B:H.249, B:H.292 Hydrogen bonds: A:Q.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bamford, V.A. et al., Structure and Spectroscopy of the Periplasmic Cytochrome C Nitrite Reductase from Escherichia Coli. Biochemistry (2002)

Release Date

2002-03-08

Peptides

CYTOCHROME C552: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

CYTOCHROME C552

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