SMTL ID : 5obo.1

Crystal structure of nitrite bound D97N mutant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-trimer

Ligands

6 x CU: COPPER (II) ION(Non-covalent)

CU.1: 4 residues within 4Å: Chain A: H.94, C.135, H.143, M.148 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.94, A:C.135, A:H.143 CU.2: 6 residues within 4Å: Chain A: N.97, H.99, H.134 Chain C: H.240, H.289 Ligands: NO2.6 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.99, A:H.134, C:H.289 CU.7: 4 residues within 4Å: Chain B: H.94, C.135, H.143, M.148 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.94, B:C.135, B:H.143 CU.8: 6 residues within 4Å: Chain A: H.240, H.289 Chain B: N.97, H.99, H.134 Ligands: NO2.12 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.289, B:H.99, B:H.134 CU.13: 4 residues within 4Å: Chain C: H.94, C.135, H.143, M.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.94, C:C.135, C:H.143 CU.14: 6 residues within 4Å: Chain B: H.240, H.289 Chain C: N.97, H.99, H.134 Ligands: NO2.18 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.99, C:H.134, B:H.289

3 x HEC: HEME C(Non-covalent)

HEC.3: 27 residues within 4Å: Chain A: T.363, C.364, V.366, C.367, H.368, V.378, P.380, P.381, L.382, S.385, F.387, L.388, I.398, V.399, L.403, N.404, G.405, I.407, V.409, Y.414, D.415, S.416, V.417, M.418, M.421, I.432 Chain B: M.92 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:V.366, A:P.380, A:L.382, A:F.387, A:I.398, A:I.398, A:V.399, A:I.407, A:V.409, A:M.418, A:I.432 Hydrogen bonds: A:S.385, A:L.388, A:S.416 Metal complexes: A:H.368 HEC.9: 27 residues within 4Å: Chain B: T.363, C.364, V.366, C.367, H.368, V.378, P.380, P.381, L.382, S.385, F.387, L.388, I.398, V.399, L.403, N.404, G.405, I.407, V.409, Y.414, D.415, S.416, V.417, M.418, M.421, I.432 Chain C: M.92 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:V.366, B:P.380, B:L.382, B:F.387, B:I.398, B:I.398, B:V.399, B:I.407, B:V.409, B:M.418, B:I.432 Hydrogen bonds: B:S.385, B:L.388, B:S.416 Metal complexes: B:H.368 HEC.15: 27 residues within 4Å: Chain A: M.92 Chain C: T.363, C.364, V.366, C.367, H.368, V.378, P.380, P.381, L.382, S.385, F.387, L.388, I.398, V.399, L.403, N.404, G.405, I.407, V.409, Y.414, D.415, S.416, V.417, M.418, M.421, I.432 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:V.366, C:P.380, C:L.382, C:F.387, C:I.398, C:I.398, C:V.399, C:I.407, C:V.409, C:M.418, C:I.432 Hydrogen bonds: C:S.385, C:L.388, C:S.416 Metal complexes: C:H.368

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: Q.258, V.261, T.263, T.264, L.265 Chain B: Y.251, P.267 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.258, A:L.265 Water bridges: A:Y.251, A:T.263, B:Y.251 GOL.5: 3 residues within 4Å: Chain A: H.165, E.166, Y.167 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.165, A:E.166, A:Y.167 Water bridges: A:V.27, A:D.164 GOL.10: 7 residues within 4Å: Chain B: Q.258, V.261, T.263, T.264, L.265 Chain C: Y.251, P.267 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.258, B:L.265 Water bridges: B:Y.251, B:T.263, C:Y.251 GOL.11: 3 residues within 4Å: Chain B: H.165, E.166, Y.167 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.166, B:Y.167, B:Y.167 Water bridges: B:V.27, B:D.164 GOL.16: 7 residues within 4Å: Chain A: Y.251, P.267 Chain C: Q.258, V.261, T.263, T.264, L.265 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.258, C:L.265 Water bridges: C:Y.251, C:T.263, C:T.264, A:Y.251 GOL.17: 3 residues within 4Å: Chain C: H.165, E.166, Y.167 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.165, C:E.166, C:Y.167 Water bridges: C:V.27, C:D.164

3 x NO2: NITRITE ION(Non-covalent)

NO2.6: 8 residues within 4Å: Chain A: N.97, H.99, H.134 Chain C: H.240, I.242, H.289, I.291 Ligands: CU.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.97 NO2.12: 8 residues within 4Å: Chain A: H.240, I.242, H.289, I.291 Chain B: N.97, H.99, H.134 Ligands: CU.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.97 NO2.18: 8 residues within 4Å: Chain B: H.240, I.242, H.289, I.291 Chain C: N.97, H.99, H.134 Ligands: CU.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.97, C:H.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, J. et al., Activation of redox tyrosine switch is required for ligand binding at the catalytic site in heme-cu nitrite reductases. To be published

Release Date

2018-08-01

Peptides

Nitrite reductase, copper-containing: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrite reductase, copper-containing

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