SMTL ID : 6f1q.1

Crystal structure of three-domain heme-Cu nitrite reductase from Ralstonia pickettii in I213 space group

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 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: 5 residues within 4Å: Chain A: D.97, H.99, H.134 Chain C: H.240, H.289 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:H.99, A:H.134, C:H.289, H2O.2, H2O.41 CU.4: 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.5: 5 residues within 4Å: Chain A: H.240, H.289 Chain B: D.97, H.99, H.134 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.289, B:H.99, B:H.134, H2O.7, H2O.19 CU.7: 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.8: 5 residues within 4Å: Chain B: H.240, H.289 Chain C: D.97, H.99, H.134 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.99, C:H.134, B:H.289, H2O.24, H2O.36

3 x HEC: HEME C(Non-covalent)

HEC.3: 25 residues within 4Å: Chain A: T.363, C.364, V.366, 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 Chain B: M.92 13 PLIP interactions: 13 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:M.418, A:I.432 Hydrogen bonds: A:S.385, A:L.388, A:S.416 Metal complexes: A:H.368 HEC.6: 25 residues within 4Å: Chain B: T.363, C.364, V.366, 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 Chain C: M.92 13 PLIP interactions: 13 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:M.418, B:I.432 Hydrogen bonds: B:S.385, B:L.388, B:S.416 Metal complexes: B:H.368 HEC.9: 25 residues within 4Å: Chain A: M.92 Chain C: T.363, C.364, V.366, 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:V.366, 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:S.416 Metal complexes: C:H.368

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, J. et al., Substrate entry and binding requires activation of tyrosine in heme-copper nitrite reductase. To be published

Release Date

2018-06-27

Peptides

Nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrite reductase

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