SMTL ID : 4wjy.1

Esherichia coli nitrite reductase NrfA H264N

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

HEC.1: 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, N.238, A.360, H.362 Ligands: HEC.3 21 PLIP interactions: 20 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:F.192, A:V.199, A:N.238 Hydrogen bonds: A:N.63, A:N.63, A:N.238 Water bridges: A:R.80, A:A.360, A:H.362 Salt bridges: A:R.80, A:H.362 Metal complexes: H2O.12 HEC.2: 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.3 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:I.257, A:I.277 Hydrogen bonds: A:Q.26, 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.3: 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: HEC.1, HEC.2, HEC.4, CA.7 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: 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.4: 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: HEC.3, HEC.5, CA.7 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:H.187, A:E.240, A:W.244, A:W.244, 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.5: 20 residues within 4Å: Chain A: I.248, H.249, N.252, V.254, D.258, P.280, F.281, T.287, C.288, C.291, H.292, V.302, V.303, R.306, M.366 Chain B: H.292, Q.294 Ligands: HEC.4, EDO.8, HEC.14 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:N.252, A:V.254, A:P.280, A:F.281, A:V.302, A:V.303 Water bridges: A:R.306, A:R.306, A:E.370 Salt bridges: A:R.306, B:H.292 Metal complexes: A:H.249, A:H.292 Hydrogen bonds: B:Q.294 HEC.10: 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, N.238, A.360, H.362 Ligands: HEC.12 20 PLIP interactions: 19 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:P.65, B:V.75, B:T.78, B:T.81, B:L.92, B:Y.190, B:Y.190, B:F.192, B:F.192, B:V.199, B:N.238 Hydrogen bonds: B:N.63, B:N.63, B:N.238 Water bridges: B:R.80, B:E.240, B:A.360 Salt bridges: B:R.80, B:H.362 Metal complexes: H2O.23 HEC.11: 22 residues within 4Å: Chain B: 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.12 23 PLIP interactions: 23 interactions with chain B, Hydrophobic interactions: B:H.23, B:Q.26, B:Y.27, B:W.30, B:L.132, B:F.145, B:F.145, B:P.150, B:L.152, B:L.152, B:I.257 Hydrogen bonds: B:Q.26, B:Q.179, B:T.273, B:T.273 Water bridges: B:R.175, B:T.273 Salt bridges: B:R.175, B:K.263, B:K.263, B:H.275 Metal complexes: B:H.138, B:H.275 HEC.12: 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, R.156, V.182, C.183, C.186, H.187, C.256, I.257, H.260, M.261, I.277 Ligands: HEC.10, HEC.11, HEC.13, CA.16 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: 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.13: 25 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, K.307, H.362, G.363, H.365, M.366, H.367 Ligands: HEC.12, HEC.14, CA.16 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:H.187, B:E.240, B:E.240, B:W.244, B:W.244, B:H.249, B:P.280, B:F.281 Hydrogen bonds: B:N.279 Salt bridges: B:H.365 Metal complexes: B:H.260, B:H.367 HEC.14: 19 residues within 4Å: Chain A: 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, R.306, M.366 Ligands: HEC.5, EDO.8, HEC.13 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 Water bridges: B:I.248, B:R.306 Salt bridges: B:R.306, A:H.292 Metal complexes: B:H.249, B:H.292 Hydrogen bonds: A:Q.294

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.3, H2O.7 CA.7: 3 residues within 4Å: Chain A: P.65 Ligands: HEC.3, HEC.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:P.65, H2O.6, H2O.7, H2O.8, H2O.12 CA.15: 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.17, H2O.20 CA.16: 3 residues within 4Å: Chain B: P.65 Ligands: HEC.12, HEC.13 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:P.65, H2O.23, H2O.24, H2O.26

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

EDO.8: 4 residues within 4Å: Chain A: C.291, H.292 Ligands: HEC.5, HEC.14 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:Q.294, A:Q.294 Hydrogen bonds: A:H.292 EDO.9: 6 residues within 4Å: Chain A: F.281, D.282, N.283, F.284, A.285, K.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.282, A:F.284, A:K.296 EDO.17: 5 residues within 4Å: Chain B: R.48, D.319, V.322, H.323, I.408 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lockwood, C.W. et al., Resolution of key roles for the distal pocket histidine in cytochrome C nitrite reductases. J.Am.Chem.Soc. (2015)

Release Date

2015-03-11

Peptides

Cytochrome c-552: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cytochrome c-552