SMTL ID : 7aqa.1

Pseudomonas stutzeri nitrous oxide reductase mutant, H382A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

1 x K7E: sulfanyl-(tricuprio-$l^{4}-sulfanyl)copper(Non-covalent)

K7E.1: 9 residues within 4Å: Chain A: H.129, H.130, H.178, N.241, H.326, H.433, K.454, H.494 Chain B: F.621 7 PLIP interactions: 7 interactions with chain A Metal complexes: A:H.129, A:H.130, A:H.178, A:H.326, A:H.433, A:H.433, A:H.494

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

B3P.2: 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.592 Hydrogen bonds: A:H.590, A:T.605 Water bridges: A:N.111, A:R.114, 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 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Water bridges: A:L.124, B:N.111, B:R.114, B:R.114, B:T.605 Hydrophobic interactions: B:V.592, B:F.606 Hydrogen bonds: B:T.605

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

NA.3: 1 residues within 4Å: Chain A: M.168 4 PLIP interactions: 4 interactions with chain A Water bridges: A:M.168, A:M.168, A:M.168, A:T.170

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.24

2 x K: POTASSIUM ION(Non-covalent)

K.5: 2 residues within 4Å: Chain A: K.454, E.469 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.469, H2O.1, H2O.2, H2O.24, H2O.25 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.2, H2O.24

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.433 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: R.388, N.390, K.403 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain B: R.181, N.241, G.327, C.328, N.329, H.433 Ligand excluded by PLIP

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

CUA.8: 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.16: 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

1 x PHE: PHENYLALANINE(Non-covalent)

PHE.9: 2 residues within 4Å: Chain B: P.642, Q.643 0 PLIP interactions:

1 x RUQ: (dicuprio-$l^{3}-sulfanyl)-sulfanyl-copper(Non-covalent)

RUQ.10: 9 residues within 4Å: Chain A: F.621 Chain B: H.129, H.130, H.178, N.241, H.326, H.433, K.454, H.494 6 PLIP interactions: 6 interactions with chain B Salt bridges: B:D.240 Metal complexes: B:H.129, B:H.130, B:H.178, B:H.433, B:H.494

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

FMT.14: 7 residues within 4Å: Chain A: W.615 Chain B: E.196, F.197, I.198, N.238, Y.256, N.257 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.198, B:N.238, B:N.257

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