SMTL ID : 6y72.1

Pseudomonas stutzeri nitrous oxide reductase mutant, H178A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 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.8 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.11: 9 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 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 NA: SODIUM ION(Non-functional Binders)

NA.2: 1 residues within 4Å: Chain A: M.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.168, A:M.168 NA.3: 1 residues within 4Å: Chain A: N.173 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.173, A:N.203, A:N.203

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 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.12: 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.25

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

FMT.5: 2 residues within 4Å: Chain A: H.115, G.118 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.115, A:D.119 FMT.6: 3 residues within 4Å: Chain A: R.388, N.390, K.403 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.388, A:K.403, A:D.479 FMT.7: 1 residues within 4Å: Chain A: I.293 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.292, A:I.293 FMT.8: 4 residues within 4Å: Chain A: T.605, F.606, V.607 Ligands: B3P.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.607 FMT.14: 6 residues within 4Å: Chain A: W.615 Chain B: E.196, F.197, I.198, N.238, N.257 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.198, B:N.238, B:N.257 FMT.15: 3 residues within 4Å: Chain B: W.510, D.511, R.512 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.511, B:R.512 FMT.16: 6 residues within 4Å: Chain B: S.134, M.135, T.136, D.141, T.188, A.224 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.135, B:T.188, B:T.188

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

CL.9: 6 residues within 4Å: Chain A: R.181, N.241, G.327, C.328, N.329, H.382 Ligand excluded by PLIP

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

CUA.10: 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.17: 7 residues within 4Å: Chain B: H.583, C.618, W.620, F.621, C.622, H.626, M.629 7 PLIP interactions: 7 interactions with chain B Metal complexes: B:H.583, B:C.618, B:C.618, B:W.620, B:C.622, B:C.622, B:H.626

1 x K: POTASSIUM ION(Non-covalent)

K.13: 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.5, H2O.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., A [3Cu:2S] cluster provides insight into the assembly and function of the Cu Z site of nitrous oxide reductase. Chem Sci (2021)

Release Date

2021-01-27

Peptides

Nitrous-oxide reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitrous-oxide reductase