SMTL ID : 7aq2.1

Pseudomonas stutzeri nitrous oxide reductase mutant, H583A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.326, H.382, H.433, H.494 Ligands: ZN.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.326, A:H.382, H2O.14, H2O.15 ZN.2: 5 residues within 4Å: Chain A: H.130, N.241, H.433, H.494 Ligands: ZN.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.130, A:H.433, A:H.494, H2O.14

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

B3P.3: 10 residues within 4Å: Chain A: L.109, R.114, H.590, G.591, V.592, T.605, F.606 Chain B: K.122, F.123, L.124 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.592, A:F.606 Hydrogen bonds: A:T.605 Water bridges: A:N.111, A:R.114, A:H.590, A:T.605 B3P.9: 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 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:H.590, B:T.605, B:V.607

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

NA.4: 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.10: 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

1 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 Hydrogen bonds: A:H.115 Water bridges: A:D.119

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

CL.6: 6 residues within 4Å: Chain A: R.181, N.241, G.327, C.328, N.329, H.382 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: R.388, N.390, K.403, G.478 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: R.181, N.241, G.327, C.328, N.329, H.382 Ligand excluded by PLIP

1 x CUA: DINUCLEAR COPPER ION(Covalent)

CUA.8: 6 residues within 4Å: Chain A: C.618, W.620, F.621, C.622, H.626, M.629 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.618, A:C.618, A:W.620, A:C.622, A:H.626

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 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

1 x K: POTASSIUM ION(Non-covalent)

K.12: 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.3, H2O.19

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

CUZ.14: 8 residues within 4Å: Chain B: H.129, H.130, H.178, N.241, H.326, H.382, H.433, H.494 9 PLIP interactions: 7 interactions with chain B, 2 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.31, H2O.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Histidine-Gated Proton-Coupled Electron Transfer to the Cu A Site of Nitrous Oxide Reductase. J.Am.Chem.Soc. (2021)

Release Date

2021-01-13

Peptides

Nitrous-oxide reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitrous-oxide reductase