SMTL ID : 2rf7.1 (1 other biounit)

Crystal structure of the escherichia coli nrfa mutant Q263E

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.179, Y.180, K.225, E.227 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.179, A:E.179, A:Y.180, A:K.225, A:E.227 CA.2: 3 residues within 4Å: Chain A: P.55 Ligands: HEC.5, HEC.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.55 CA.11: 4 residues within 4Å: Chain B: E.179, Y.180, K.225, E.227 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.179, B:Y.180, B:K.225, B:E.227, H2O.22 CA.12: 3 residues within 4Å: Chain B: P.55 Ligands: HEC.15, HEC.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:P.55

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

HEC.3: 20 residues within 4Å: Chain A: Y.52, N.53, P.55, D.64, V.65, T.68, R.70, T.71, L.82, C.86, C.89, K.90, C.176, H.177, Y.180, F.182, V.189, H.228, H.352 Ligands: HEC.5 24 PLIP interactions: 23 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:P.55, A:V.65, A:T.68, A:T.71, A:L.82, A:Y.180, A:Y.180, A:Y.180, A:F.182, A:F.182, A:V.189, A:V.189, A:H.228 Hydrogen bonds: A:N.53, A:N.53, A:A.350 Water bridges: A:Y.52, A:Y.52, A:R.70 Salt bridges: A:R.70, A:H.228, A:H.352 pi-Stacking: A:H.228 Metal complexes: H2O.16 HEC.4: 24 residues within 4Å: Chain A: F.9, H.13, Q.16, Y.17, W.20, L.122, G.123, C.124, C.127, H.128, F.135, G.138, P.140, L.142, R.165, Q.169, I.247, M.251, K.253, Y.262, T.263, H.265, I.267 Ligands: HEC.5 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:F.9, A:H.13, A:Q.16, A:Q.16, A:Y.17, A:W.20, A:L.122, A:F.135, A:P.140, A:L.142, A:L.142, A:I.247, A:T.263, A:I.267 Hydrogen bonds: A:Q.169, A:T.263 Water bridges: A:R.165, A:K.253, A:T.263 Salt bridges: A:R.165, A:K.253, A:K.253 Metal complexes: A:H.128, A:H.265 HEC.5: 25 residues within 4Å: Chain A: Q.26, P.55, R.56, G.57, H.58, F.60, A.61, D.64, C.89, K.90, L.122, R.146, V.172, C.173, C.176, H.177, I.247, H.250, M.251, I.267, G.268 Ligands: CA.2, HEC.3, HEC.4, HEC.6 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:P.55, A:A.61, A:K.90, A:L.122, A:I.247, A:H.250, A:I.267 Hydrogen bonds: A:Q.26, A:F.60, A:D.64 Metal complexes: A:H.58, A:H.177 HEC.6: 22 residues within 4Å: Chain A: P.55, C.173, H.177, E.230, W.234, H.239, V.244, T.245, C.246, C.249, H.250, N.269, P.270, F.271, V.293, G.353, H.355, M.356, H.357 Ligands: CA.2, HEC.5, HEC.7 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:H.177, A:E.230, A:W.234, A:W.234, A:H.239, A:P.270, A:F.271 Hydrogen bonds: A:N.269 Salt bridges: A:H.355 Metal complexes: A:H.250, A:H.357 HEC.7: 21 residues within 4Å: Chain A: I.238, H.239, N.242, V.244, D.248, C.249, P.270, F.271, T.277, C.278, C.281, H.282, V.292, V.293, R.296, M.356 Chain B: I.238, H.282, Q.284 Ligands: HEC.6, HEC.17 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:N.242, A:V.244, A:V.244, A:P.270, A:F.271, A:V.292, A:V.293, B:I.238 Water bridges: A:I.238, A:I.238, A:R.296, A:R.296 Salt bridges: A:R.296, B:H.282 Metal complexes: A:H.239, A:H.282 Hydrogen bonds: B:Q.284 HEC.13: 23 residues within 4Å: Chain B: Y.52, N.53, P.55, D.64, V.65, T.68, R.70, T.71, L.82, A.85, C.86, C.89, K.90, C.176, H.177, V.178, Y.180, F.182, V.189, H.228, A.350, H.352 Ligands: HEC.15 22 PLIP interactions: 21 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:P.55, B:V.65, B:T.68, B:T.71, B:L.82, B:V.178, B:Y.180, B:Y.180, B:Y.180, B:F.182, B:V.189, B:H.228 Hydrogen bonds: B:N.53, B:N.53, B:A.350 Water bridges: B:R.70, B:H.352 Salt bridges: B:R.70, B:H.228, B:H.352 pi-Stacking: B:H.228 Metal complexes: H2O.35 HEC.14: 25 residues within 4Å: Chain B: F.9, H.13, Q.16, Y.17, W.20, L.122, G.123, C.124, C.127, H.128, F.135, G.138, P.140, L.142, R.165, Q.169, V.172, I.247, M.251, K.253, Y.262, T.263, H.265, I.267 Ligands: HEC.15 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:F.9, B:H.13, B:Q.16, B:Q.16, B:Y.17, B:W.20, B:L.122, B:F.135, B:F.135, B:L.142, B:V.172, B:I.247, B:I.267 Hydrogen bonds: B:Q.169, B:T.263 Water bridges: B:R.165, B:T.263, B:T.263 Salt bridges: B:R.165, B:K.253, B:K.253 Metal complexes: B:H.128, B:H.265 HEC.15: 26 residues within 4Å: Chain B: Q.26, P.55, R.56, G.57, H.58, F.60, A.61, D.64, C.89, K.90, L.122, R.146, V.172, C.173, C.176, H.177, C.246, I.247, H.250, M.251, I.267, G.268 Ligands: CA.12, HEC.13, HEC.14, HEC.16 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:P.55, B:A.61, B:K.90, B:L.122, B:L.122, B:I.247, B:H.250, B:I.267, B:I.267 Hydrogen bonds: B:Q.26, B:R.56, B:F.60, B:D.64 Metal complexes: B:H.58, B:H.177 HEC.16: 23 residues within 4Å: Chain B: C.173, H.177, E.230, Y.231, W.234, H.239, V.244, T.245, C.246, C.249, H.250, N.269, P.270, F.271, V.293, H.352, G.353, H.355, M.356, H.357 Ligands: CA.12, HEC.15, HEC.17 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:H.177, B:E.230, B:W.234, B:H.239, B:P.270, B:F.271 Hydrogen bonds: B:N.269 Salt bridges: B:K.297, B:H.355 Metal complexes: B:H.250, B:H.357 HEC.17: 21 residues within 4Å: Chain A: I.238, H.282, Q.284 Chain B: I.238, H.239, N.242, V.244, D.248, C.249, P.270, F.271, T.277, C.278, C.281, H.282, V.292, R.296, M.356 Ligands: HEC.7, HEC.16, EDO.24 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:I.238, B:I.238, B:N.242, B:V.244, B:V.244, B:P.270, B:F.271, B:V.292 Water bridges: B:H.282, B:R.296, A:H.282, A:H.282 Salt bridges: B:R.296, A:H.282 Metal complexes: B:H.239, B:H.282 Hydrogen bonds: A:Q.284

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

EDO.8: 6 residues within 4Å: Chain A: F.271, D.272, N.273, F.274, A.275, K.286 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.272, A:F.274 EDO.9: 7 residues within 4Å: Chain A: M.197, K.198, V.199, E.232, T.233, E.361, M.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.199, A:E.232 EDO.10: 5 residues within 4Å: Chain A: D.375, T.378, K.379, R.382 Chain B: R.377 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:K.379, A:R.382, A:R.382, B:R.377 Water bridges: A:K.379, B:R.377, B:R.377 EDO.18: 6 residues within 4Å: Chain B: F.271, D.272, N.273, F.274, A.275, K.286 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.272, B:N.273, B:F.274, B:A.275 EDO.19: 3 residues within 4Å: Chain B: F.160, E.161, Q.168 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.168 Water bridges: B:T.143 EDO.20: 8 residues within 4Å: Chain B: M.197, K.198, V.199, E.232, T.233, L.347, E.361, M.365 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.199, B:E.232, B:E.361 EDO.21: 5 residues within 4Å: Chain B: V.62, T.63, R.66, N.121, E.431 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.66, B:N.121, B:E.431 Water bridges: B:V.62, B:R.66, B:N.121 EDO.22: 4 residues within 4Å: Chain B: A.210, S.212, P.222, R.339 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.210 Water bridges: B:K.332, B:D.336 EDO.23: 5 residues within 4Å: Chain B: S.19, V.254, Y.262, D.264, K.266 No protein-ligand interaction detected (PLIP) EDO.24: 5 residues within 4Å: Chain B: D.248, T.277, N.280, C.281 Ligands: HEC.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.248, B:N.280

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
A

B
B

Cytochrome c-552

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