SMTL ID : 5ocf.1

Crystal structure of nitric oxide bound to three-domain heme-Cu nitrite reductase from Ralstonia pickettii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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: D.97, H.99, H.134 Chain C: H.240, H.289 Ligands: NO.4 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: C:H.289, A:H.99, A:H.134, NO.4 CU.5: 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.6: 6 residues within 4Å: Chain A: H.240, H.289 Chain B: D.97, H.99, H.134 Ligands: NO.8 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:H.99, B:H.134, A:H.289, NO.8 CU.9: 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.10: 6 residues within 4Å: Chain B: H.240, H.289 Chain C: D.97, H.99, H.134 Ligands: NO.12 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: C:H.99, C:H.134, B:H.289, NO.12

3 x HEC: HEME C(Non-covalent)

HEC.3: 23 residues within 4Å: Chain A: T.363, C.364, C.367, H.368, P.380, P.381, L.382, S.385, F.387, L.388, I.398, V.399, L.403, N.404, G.405, V.409, Y.414, D.415, S.416, V.417, M.418, M.421, I.432 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:P.380, A:L.382, A:F.387, A:I.398, A:I.398, A:V.399, A:M.418, A:I.432 Hydrogen bonds: A:S.385, A:L.388, A:L.403, A:S.416 Metal complexes: A:H.368 HEC.7: 23 residues within 4Å: Chain B: T.363, C.364, C.367, H.368, P.380, P.381, L.382, S.385, F.387, L.388, I.398, V.399, L.403, N.404, G.405, V.409, Y.414, D.415, S.416, V.417, M.418, M.421, I.432 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:P.380, B:L.382, B:F.387, B:I.398, B:I.398, B:V.399, B:M.418, B:I.432 Hydrogen bonds: B:S.385, B:L.388, B:L.403, B:S.416 Metal complexes: B:H.368 HEC.11: 23 residues within 4Å: Chain C: T.363, C.364, C.367, H.368, P.380, P.381, L.382, S.385, F.387, L.388, I.398, V.399, L.403, N.404, G.405, V.409, Y.414, D.415, S.416, V.417, M.418, M.421, I.432 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:P.380, C:L.382, C:F.387, C:I.398, C:I.398, C:V.399, C:M.418, C:I.432 Hydrogen bonds: C:S.385, C:L.388, C:L.403, C:S.416 Metal complexes: C:H.368

3 x NO: NITRIC OXIDE(Non-covalent)

NO.4: 8 residues within 4Å: Chain A: D.97, H.99, H.134 Chain C: H.240, I.242, H.289, I.291 Ligands: CU.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.97, A:D.97 NO.8: 8 residues within 4Å: Chain A: H.240, I.242, H.289, I.291 Chain B: D.97, H.99, H.134 Ligands: CU.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.97, A:H.240 Water bridges: B:D.97 NO.12: 8 residues within 4Å: Chain B: H.240, I.242, H.289, I.291 Chain C: D.97, H.99, H.134 Ligands: CU.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.97, C:D.97

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

2018-06-27

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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