SMTL ID : 6rl0.1 (1 other biounit)

Recombinant Pseudomonas stutzeri nitrous oxide reductase, form I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.1: 10 residues within 4Å: Chain A: L.109, R.114, H.590, G.591, V.592, T.605 Chain B: K.122, F.123, L.124 Ligands: FMT.6 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:L.124, A:N.111, A:R.114, A:T.605 Hydrophobic interactions: A:V.592 B3P.9: 10 residues within 4Å: Chain A: K.122, F.123 Chain B: L.109, R.114, H.590, G.591, V.592, T.605, F.606 Ligands: FMT.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.592, B:F.606 Hydrogen bonds: B:T.605 Water bridges: B:N.111, B:R.114, B:H.590, B:T.605

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: R.181, N.241, G.327, C.328, N.329, H.382 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: R.181, N.241, G.327, C.328, N.329, H.382 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: Y.256, E.259, M.267, D.273, N.324 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.259, A:E.259, A:M.267, A:D.273, A:D.273 CA.11: 5 residues within 4Å: Chain B: Y.256, E.259, M.267, D.273, N.324 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.259, B:M.267, B:D.273, B:D.273, H2O.18

2 x CUK: [4Cu:2S] cluster(Non-covalent)

CUK.4: 12 residues within 4Å: Chain A: H.129, H.130, H.178, N.241, H.326, H.382, G.432, H.433, K.454, H.494 Chain B: F.621, M.627 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:H.129, A:H.130, A:H.178, A:H.326, A:H.382, A:H.433 CUK.12: 10 residues within 4Å: Chain A: F.621 Chain B: H.129, H.130, H.178, N.241, H.326, G.432, H.433, K.454, H.494 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:H.129, B:H.130, B:H.178, B:H.326, B:H.433, B:H.494

2 x CUA: DINUCLEAR COPPER ION(Non-covalent)

CUA.5: 7 residues within 4Å: Chain A: H.583, C.618, W.620, F.621, C.622, H.626, M.629 7 PLIP interactions: 7 interactions with chain A Metal complexes: A:H.583, A:C.618, A:C.618, A:W.620, A:C.622, A:C.622, A:H.626 CUA.13: 7 residues within 4Å: Chain B: H.583, C.618, W.620, F.621, C.622, H.626, M.629 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:C.618, B:C.618, B:W.620, B:C.622, B:C.622, B:H.626

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 3 residues within 4Å: Chain A: F.606, V.607 Ligands: B3P.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.607 Water bridges: A:D.609 FMT.14: 3 residues within 4Å: Chain B: F.606, V.607 Ligands: B3P.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.607

2 x K: POTASSIUM ION(Non-covalent)

K.7: 2 residues within 4Å: Chain A: K.454, E.469 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:K.454, A:E.469, H2O.10, H2O.18, H2O.22 K.15: 2 residues within 4Å: Chain B: K.454, E.469 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:K.454, B:E.469, H2O.2, H2O.7, H2O.20

2 x NA: SODIUM ION(Non-functional Binders)

NA.8: 2 residues within 4Å: Chain A: I.116, M.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.116, A:M.168 Water bridges: A:T.170 NA.16: 1 residues within 4Å: Chain B: M.168 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.116, B:M.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Functional assembly of nitrous oxide reductase provides insights into copper site maturation. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-06-26

Peptides

Nitrous-oxide reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Nitrous-oxide reductase

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