SMTL ID : 6rkz.1

Recombinant Pseudomonas stutzeri nitrous oxide reductase, form II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: 9 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.592 Hydrogen bonds: A:T.605 Water bridges: A:N.111, A:R.114, A:R.114, A:H.590, A:T.605 B3P.15: 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.21 8 PLIP interactions: 8 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:R.114, B:H.590, B:T.605

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

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

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.17: 5 residues within 4Å: Chain B: Y.256, E.259, M.267, D.273, N.324 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.259, B:E.259, B:M.267, B:D.273, B:D.273

2 x K: POTASSIUM ION(Non-covalent)

K.4: 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.2, H2O.21, H2O.25 K.18: 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.3, H2O.8, H2O.27

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

FMT.5: 1 residues within 4Å: Chain A: K.525 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.525 FMT.6: 3 residues within 4Å: Chain A: Y.429, D.458, R.459 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.458, A:R.459 FMT.7: 3 residues within 4Å: Chain A: D.333, G.334, K.335 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.335 FMT.8: 7 residues within 4Å: Chain A: S.134, M.135, T.136, D.141, K.143, H.187, T.188 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.135, A:T.136, A:T.188 Water bridges: A:K.143, A:K.143 FMT.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.10: 3 residues within 4Å: Chain A: D.291, F.292, I.293 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.291, A:D.291, A:F.292, A:I.293 FMT.19: 4 residues within 4Å: Chain A: H.623 Chain B: F.396, Q.430, F.455 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.623, A:H.623 FMT.20: 6 residues within 4Å: Chain B: V.521, A.524, K.525, I.529, N.530, L.531 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.529, B:N.530, B:L.531 FMT.21: 3 residues within 4Å: Chain B: F.606, V.607 Ligands: B3P.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.607

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

CL.11: 6 residues within 4Å: Chain A: R.181, N.241, G.327, C.328, N.329, H.382 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: R.388, N.390, K.403, D.479 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain B: R.181, N.241, G.327, C.328, N.329, H.382 Ligand excluded by PLIP

2 x CUZ: (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION(Non-covalent)

CUZ.13: 8 residues within 4Å: Chain A: H.129, H.130, H.178, N.241, H.326, H.382, H.433, H.494 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.129, A:H.130, A:H.178, A:H.326, A:H.382, A:H.433, A:H.494, H2O.15 CUZ.23: 8 residues within 4Å: Chain B: H.129, H.130, H.178, N.241, H.326, H.382, H.433, H.494 8 PLIP interactions: 7 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.129, B:H.130, B:H.178, B:H.326, B:H.382, B:H.433, B:H.494, H2O.33

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

CUA.14: 7 residues within 4Å: Chain A: H.583, C.618, W.620, F.621, C.622, H.626, M.629 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:C.618, A:C.618, A:W.620, A:C.622, A:C.622, A:H.626 CUA.24: 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

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
B

Nitrous-oxide reductase

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