SMTL ID : 6qq5.1

Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) from Alcaligenes xylosoxidans

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)(Covalent)

HEM.1: 23 residues within 4Å: Chain A: G.76, A.77, Y.78, Q.296, G.300, G.301, A.304, Y.324, R.328, H.331, A.335, I.339, E.407, Y.408, A.630, H.631, L.634, F.635, R.720, D.724, F.727 Ligands: HEM.2, CA.4 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:A.304, A:A.335, A:I.339, A:Y.408, A:A.630, A:F.635, A:F.727, A:F.727, A:F.727 Hydrogen bonds: A:Y.78, A:Y.78, A:Y.324 Salt bridges: A:R.328, A:R.328 Metal complexes: A:H.331 HEM.2: 25 residues within 4Å: Chain A: Y.78, E.407, Y.408, W.482, E.490, H.537, H.538, S.556, E.559, V.560, A.604, G.608, I.611, N.612, L.617, Q.621, T.626, H.629, A.630, A.633, L.634, Y.638 Ligands: HEM.1, FE.3, CA.4 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:W.482, A:E.490, A:V.560, A:I.611, A:N.612, A:L.617, A:T.626, A:A.630, A:A.633, A:L.634 Hydrogen bonds: A:Y.78, A:Y.408, A:Q.621, A:T.626 pi-Cation interactions: A:H.486, A:H.538 Metal complexes: A:H.629 HEM.5: 23 residues within 4Å: Chain B: G.76, A.77, Y.78, Q.296, G.300, A.304, Y.324, R.328, H.331, A.335, W.338, I.339, E.407, Y.408, A.630, H.631, L.634, M.678, R.720, D.724, F.727 Ligands: HEM.6, CA.8 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:A.304, B:A.335, B:W.338, B:I.339, B:Y.408, B:A.630, B:L.634, B:F.727 Hydrogen bonds: B:Y.78, B:Y.78, B:Y.324 Salt bridges: B:R.328, B:R.328 pi-Cation interactions: B:H.631 Metal complexes: B:H.631 HEM.6: 27 residues within 4Å: Chain B: H.75, Y.78, E.407, Y.408, W.482, E.490, H.537, H.538, S.556, E.559, V.560, N.600, A.604, G.608, I.611, N.612, L.617, Q.621, T.626, H.629, A.630, A.633, L.634, Y.638 Ligands: HEM.5, FE.7, CA.8 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.482, B:E.490, B:V.560, B:I.611, B:N.612, B:L.617, B:T.626, B:A.630, B:A.633, B:L.634 Hydrogen bonds: B:Y.78, B:Y.408, B:Q.621, B:T.626 pi-Cation interactions: B:H.486, B:H.486, B:H.538 Metal complexes: B:H.629

2 x FE: FE (III) ION(Non-covalent)

FE.3: 4 residues within 4Å: Chain A: H.486, H.537, H.538 Ligands: HEM.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.486, A:H.486, A:H.537, A:H.538 FE.7: 4 residues within 4Å: Chain B: H.486, H.537, H.538 Ligands: HEM.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.486, B:H.486, B:H.537, B:H.538

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: G.76, Y.78, R.328, E.407 Ligands: HEM.1, HEM.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:G.76, A:Y.78, A:E.407, A:E.407 CA.8: 6 residues within 4Å: Chain B: G.76, Y.78, R.328, E.407 Ligands: HEM.5, HEM.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:G.76, B:Y.78, B:E.407, B:E.407

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gopalasingam, C.C. et al., Dimeric structures of quinol-dependent nitric oxide reductases (qNORs) revealed by cryo-electron microscopy. Sci Adv (2019)

Release Date

2019-09-11

Peptides

Nitric oxide reductase subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Nitric oxide reductase subunit B