SMTL ID : 2yqb.1

Structure of P93A variant of three-domain heme-Cu nitrite reductase from Ralstonia pickettii at 1.4 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 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 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.99, A:H.134, C:H.289, H2O.11 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 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.99, B:H.134, A:H.289, H2O.42 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 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.289, C:H.99, C:H.134, H2O.73

3 x HEC: HEME C(Covalent)

HEC.3: 27 residues within 4Å: Chain A: T.363, C.364, V.366, C.367, H.368, F.379, 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, P.419, M.421, I.432 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:V.366, A:F.379, A:P.380, A:L.382, A:F.387, A:I.398, A:I.398, A:V.399, A:L.403, 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.6: 27 residues within 4Å: Chain B: T.363, C.364, V.366, C.367, H.368, F.379, 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, P.419, M.421, I.432 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:V.366, B:F.379, B:P.380, B:L.382, B:F.387, B:I.398, B:I.398, B:V.399, B:L.403, 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.9: 27 residues within 4Å: Chain C: T.363, C.364, V.366, C.367, H.368, F.379, 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, P.419, M.421, I.432 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:V.366, C:F.379, C:P.380, C:L.382, C:F.387, C:I.398, C:I.398, C:V.399, C:L.403, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antonyuk, S.V. et al., Structures of protein-protein complexes involved in electron transfer. Nature (2013)

Release Date

2013-04-03

Peptides

COPPER-CONTAINING NITRITE REDUCTASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

COPPER-CONTAINING NITRITE REDUCTASE