SMTL ID : 3l1t.2 (1 other biounit)

E. coli NrfA sulfite ocmplex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.189, Y.190, Y.216, K.235, A.236, 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.2, H2O.3 CA.2: 3 residues within 4Å: Chain A: P.65 Ligands: HEC.5, HEC.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.65 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.17, H2O.17 CA.16: 3 residues within 4Å: Chain B: P.65 Ligands: HEC.19, HEC.20 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:P.65, H2O.13

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

HEC.3: 22 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, SO3.8 18 PLIP interactions: 18 interactions with chain A, 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 Hydrogen bonds: A:N.63, A:N.63 Water bridges: A:E.240, A:H.362 Salt bridges: A:R.80, A:H.238, A:H.362 pi-Stacking: A:H.238 HEC.4: 23 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 Ligands: HEC.5 24 PLIP interactions: 24 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:P.150, A:L.152, A:L.152, A:I.257, A:T.273 Hydrogen bonds: A:Q.179, A:T.273, A:T.273 Water bridges: A:R.175, A:K.263, A:T.273 Salt bridges: A:R.175, A:K.263, A:K.263 Metal complexes: A:H.138, A:H.275 HEC.5: 25 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, V.182, C.183, C.186, H.187, C.256, H.260, M.261, I.277, G.278 Ligands: CA.2, HEC.3, HEC.4, HEC.6 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:P.65, A:K.100, A:L.132, A:L.132, A:H.260, A:I.277 Hydrogen bonds: A:Q.36, 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: CA.2, HEC.5, HEC.7 14 PLIP interactions: 14 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 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, F.281, T.287, C.288, C.291, H.292, L.299, V.303, R.306, M.366 Chain B: I.248, H.292, Q.294 Ligands: HEC.6, EDO.12, HEC.21 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:I.248, A:N.252, A:V.254, A:F.281, A:L.299, A:V.303, B:I.248 Salt bridges: A:R.306, B:H.292 Metal complexes: A:H.249, A:H.292 Hydrogen bonds: B:Q.294 HEC.17: 21 residues within 4Å: Chain B: Y.62, N.63, P.65, D.74, V.75, T.78, R.80, L.92, 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, SO3.22 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:P.65, B:V.75, B:T.78, B:L.92, B:Y.190, B:Y.190, B:Y.190, B:F.192, B:V.199, B:V.199, B:H.238 Hydrogen bonds: B:N.63, B:N.63, B:A.360 Water bridges: B:Y.62, B:Y.62 Salt bridges: B:R.80, B:H.238, B:H.362 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, V.182, I.257, M.261, K.263, Y.272, T.273, H.275 Ligands: HEC.19 17 PLIP interactions: 17 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:L.152, B:V.182, B:I.257 Hydrogen bonds: B:Q.179, B:T.273 Salt bridges: B:R.175, B:K.263, B:K.263 Metal complexes: B:H.138, B:H.275 HEC.19: 25 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, V.182, C.183, C.186, H.187, C.256, I.257, H.260, M.261, I.277 Ligands: CA.16, HEC.17, HEC.18, HEC.20 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:K.100, B:L.132, B:L.132, B:I.257, B:H.260, B:I.277 Hydrogen bonds: B:Q.36, B:F.70, B:D.74 Metal complexes: B:H.68, B:H.187 HEC.20: 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: CA.16, HEC.19, HEC.21 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:H.187, B:E.240, 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: 20 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, F.281, T.287, C.288, C.291, H.292, V.302, R.306, M.366 Ligands: HEC.7, EDO.12, HEC.20 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B, Hydrophobic interactions: A:I.248, B:N.252, B:V.254, B:V.254, B:F.281, B:V.302 Hydrogen bonds: A:Q.294 Salt bridges: A:H.292, B:R.306 Metal complexes: B:H.249, B:H.292

2 x SO3: SULFITE ION(Non-covalent)

SO3.8: 6 residues within 4Å: Chain A: F.58, R.80, Y.190, Q.237, H.238 Ligands: HEC.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.80, A:Y.190, A:Y.190 Water bridges: A:Q.237 SO3.22: 6 residues within 4Å: Chain B: F.58, R.80, Y.190, Q.237, H.238 Ligands: HEC.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.80, B:Y.190 Water bridges: B:R.80

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

EDO.9: 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:N.283, A:F.284, A:A.285, A:K.296 EDO.10: 4 residues within 4Å: Chain A: Y.56, Y.190, F.192, Q.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.56, A:Q.237 Water bridges: A:F.192, A:D.223 EDO.11: 6 residues within 4Å: Chain A: Q.294, A.298, L.299, V.302 Chain B: I.248, N.252 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.252 EDO.12: 7 residues within 4Å: Chain A: R.306, P.369, E.370 Chain B: R.306, E.370 Ligands: HEC.7, HEC.21 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.370, A:R.306, A:E.370, A:E.370 Water bridges: B:R.306 EDO.13: 4 residues within 4Å: Chain A: D.319, V.322, H.323, I.408 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.319, A:H.323 Water bridges: A:R.48 EDO.14: 8 residues within 4Å: Chain A: M.207, K.208, V.209, E.242, T.243, L.357, E.371, M.375 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.209, A:E.242, A:E.371 EDO.23: 5 residues within 4Å: Chain A: N.252 Chain B: Q.294, A.298, K.301, V.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.252, A:N.252 EDO.24: 6 residues within 4Å: Chain B: F.281, D.282, N.283, F.284, A.285, K.296 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.284, B:A.285, B:K.296, B:K.296

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kemp, G.L. et al., Kinetic and thermodynamic resolution of the interactions between sulfite and the pentahaem cytochrome NrfA from Escherichia coli. Biochem.J. (2010)

Release Date

2010-10-27

Peptides

Cytochrome c-552: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Cytochrome c-552

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