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

High Resolution Crystal Structure of the Escherichia coli Cytochrome c Nitrite Reductase.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.189, Y.190, 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.1, H2O.2 CA.2: 3 residues within 4Å: Chain A: P.65 Ligands: HEC.5, HEC.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:P.65, H2O.5, H2O.9, H2O.12 CA.15: 4 residues within 4Å: Chain B: E.189, Y.190, 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.20, H2O.21 CA.16: 4 residues within 4Å: Chain B: P.65, R.66 Ligands: HEC.19, HEC.20 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:P.65, H2O.28, H2O.30

10 x HEC: HEME C(Covalent)

HEC.3: 21 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, Y.190, F.192, V.199, H.238, H.362 Ligands: HEC.5 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:P.65, A:V.75, 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, A:R.80 Salt bridges: A:R.80, A:H.238, A:H.362 pi-Stacking: A:H.238 Metal complexes: H2O.3 HEC.4: 25 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, V.182, I.257, M.261, K.263, Y.272, T.273, H.275, I.277 Ligands: HEC.5 25 PLIP interactions: 25 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:F.145, A:L.152, A:L.152, A:V.182, A:I.257, A:I.277 Hydrogen bonds: A:Q.179, A:T.273 Water bridges: A:R.175, A:K.263, A:T.273, A:T.273 Salt bridges: A:R.175, A:K.263, A:K.263 Metal complexes: A:H.138, A:H.275 HEC.5: 26 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, R.156, V.182, C.183, C.186, H.187, C.256, I.257, H.260, M.261, I.277, G.278 Ligands: CA.2, HEC.3, HEC.4, HEC.6 14 PLIP interactions: 14 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, A:I.277 Hydrogen bonds: A:Q.36, A:F.70, A:D.74 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: CA.2, HEC.5, HEC.7 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:H.187, A:E.240, A:W.244, A:W.244, A:H.249, A:P.280, A:F.281 Hydrogen bonds: A:N.279 Salt bridges: A:K.307, A:H.365 Metal complexes: A:H.260, A:H.367 HEC.7: 21 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.303, R.306, M.366 Chain B: I.248, H.292, Q.294 Ligands: HEC.6, EDO.10, HEC.21 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:I.248, A:I.248, A:N.252, A:V.254, A:D.258, A:P.280, A:F.281, A:V.303, B:I.248 Water bridges: A:I.248, A:I.248, A:R.306, A:R.306 Salt bridges: A:H.249, A:R.306, B:H.292 Metal complexes: A:H.249, A:H.292 Hydrogen bonds: B:Q.294 HEC.17: 22 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, C.186, H.187, Y.190, F.192, V.199, H.238, A.360, H.362 Ligands: HEC.19 22 PLIP interactions: 21 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: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:R.80, B:H.362 Salt bridges: B:R.80, B:H.238, B:H.362 pi-Stacking: B:H.238 Metal complexes: H2O.20 HEC.18: 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.19 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.19, B:H.23, B:Q.26, B:Q.26, B:Y.27, B:W.30, B:L.132, 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:T.273, B:T.273 Salt bridges: B:R.175, B:K.263, B:K.263 Metal complexes: B:H.138, B:H.275 HEC.19: 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, R.156, V.182, C.183, C.186, H.187, C.256, I.257, H.260, M.261, I.277, G.278 Ligands: CA.16, HEC.17, HEC.18, HEC.20 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: 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:R.66, B:F.70, B:D.74 Metal complexes: B:H.68, B:H.187 HEC.20: 23 residues within 4Å: Chain B: 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: CA.16, HEC.19, HEC.21 13 PLIP interactions: 13 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 Hydrogen bonds: B:N.279 Salt bridges: B:K.307, B:H.365 Metal complexes: B:H.260, B:H.367 HEC.21: 19 residues within 4Å: Chain A: H.292, Q.294 Chain B: I.248, H.249, N.252, V.254, D.258, P.280, F.281, T.287, C.288, C.291, H.292, V.303, R.306, M.366 Ligands: HEC.7, EDO.10, HEC.20 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:I.248, B:N.252, B:V.254, B:V.254, B:P.280, B:F.281, B:V.303 Water bridges: B:H.249, B:N.252, B:R.306, B:R.306, A:H.292 Salt bridges: B:H.249, B:R.306, A:H.292 Metal complexes: B:H.249, B:H.292 Hydrogen bonds: A:Q.294

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

SO4.8: 6 residues within 4Å: Chain A: F.281, D.282, N.283, F.284, A.285, K.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.284, A:A.285 Water bridges: A:K.296 Salt bridges: A:K.296 SO4.22: 6 residues within 4Å: Chain B: F.281, D.282, N.283, F.284, A.285, K.296 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.281, B:F.284, B:A.285 Water bridges: B:K.296 Salt bridges: B:K.296

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 7 residues within 4Å: Chain A: M.207, K.208, V.209, E.242, T.243, E.371, M.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.208, A:V.209, A:E.242 EDO.10: 8 residues within 4Å: Chain A: I.248, R.306, E.370 Chain B: I.248, R.306, E.370 Ligands: HEC.7, HEC.21 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.306, B:R.306, A:R.306, A:R.306 EDO.11: 4 residues within 4Å: Chain A: D.381, K.382, D.385 Chain B: K.316 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.382 Water bridges: A:D.385, B:Q.320 EDO.12: 5 residues within 4Å: Chain A: D.385, T.388, K.389, R.392 Chain B: R.387 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.389, A:R.392, A:R.392, B:R.387 Water bridges: A:K.389, B:R.387 EDO.13: 9 residues within 4Å: Chain A: C.259, H.260, D.274, K.276, I.277, G.278, N.279, P.280, N.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.260, A:D.274, A:G.278 EDO.14: 6 residues within 4Å: Chain A: R.48, D.319, V.322, H.323, I.405, I.408 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.48 EDO.23: 4 residues within 4Å: Chain B: R.39, N.63, R.66, D.74 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.39 Water bridges: B:E.38, B:K.64, B:R.66, B:D.74 EDO.24: 6 residues within 4Å: Chain A: R.387, E.402 Chain B: D.385, T.388, K.389, R.392 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.387, B:K.389, B:R.392, B:R.392 Water bridges: A:R.387 EDO.25: 8 residues within 4Å: Chain B: M.207, K.208, V.209, E.242, T.243, A.246, E.371, M.375 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.209, B:E.242, B:E.371 EDO.26: 4 residues within 4Å: Chain B: S.29, Y.272, D.274, K.276 No protein-ligand interaction detected (PLIP) EDO.27: 7 residues within 4Å: Chain B: M.94, L.107, D.111, G.115, Y.116, H.118, R.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.111 Water bridges: B:R.123 EDO.28: 6 residues within 4Å: Chain B: G.55, Y.56, P.57, S.59, R.60, L.420 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.60 Water bridges: B:S.59, B:R.60 EDO.29: 4 residues within 4Å: Chain B: D.319, V.322, H.323, I.408 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.319 Water bridges: B:R.48, B:H.323 EDO.30: 3 residues within 4Å: Chain B: E.210, E.213, R.354 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.210, B:R.354 Water bridges: A:K.316

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clarke, T.A. et al., Role of a Conserved Glutamine Residue in Tuning the Catalytic Activity of Escherichia coli Cytochrome c Nitrite Reductase. Biochemistry (2008)

Release Date

2008-03-25

Peptides

Cytochrome c-552: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Cytochrome c-552

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