SMTL ID : 9kvl.1

Neutron and X-ray joint refined structure of a copper-containing nitrite reductase (C135A mutant) in complex with nitrite

Coordinates

PDB Format Compare

Method

NEUTRON DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 8 residues within 4Å: Chain A: D.148, V.151, D.152, R.153, E.154, R.214, Y.216 Ligands: MRD.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.151 Hydrogen bonds: A:E.154, A:E.154 MPD.7: 8 residues within 4Å: Chain B: D.148, V.151, D.152, R.153, E.154, R.214, Y.216 Ligands: MRD.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.151 Hydrogen bonds: B:E.154, B:E.154 MPD.13: 8 residues within 4Å: Chain C: D.148, V.151, D.152, R.153, E.154, R.214, Y.216 Ligands: MRD.14 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.151 Hydrogen bonds: C:E.154, C:E.154

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 8 residues within 4Å: Chain A: D.148, V.151, D.152, R.153, E.154, R.214, Y.216 Ligands: MPD.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.151, A:V.151 Hydrogen bonds: A:E.154, A:E.154 MRD.8: 8 residues within 4Å: Chain B: D.148, V.151, D.152, R.153, E.154, R.214, Y.216 Ligands: MPD.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.151, B:V.151 Hydrogen bonds: B:E.154, B:E.154 MRD.14: 8 residues within 4Å: Chain C: D.148, V.151, D.152, R.153, E.154, R.214, Y.216 Ligands: MPD.13 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.151, C:V.151 Hydrogen bonds: C:E.154, C:E.154

3 x NO2: NITRITE ION(Non-covalent)

NO2.3: 10 residues within 4Å: Chain A: D.83, H.85, H.119, V.125 Chain B: H.229, V.231, V.277, H.279, F.281 Ligands: CU.5 No protein-ligand interaction detected (PLIP) NO2.9: 10 residues within 4Å: Chain B: D.83, H.85, H.119, V.125 Chain C: H.229, V.231, V.277, H.279, F.281 Ligands: CU.11 No protein-ligand interaction detected (PLIP) NO2.15: 10 residues within 4Å: Chain A: H.229, V.231, V.277, H.279, F.281 Chain C: D.83, H.85, H.119, V.125 Ligands: CU.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.119

9 x CU: COPPER (II) ION(Non-covalent)

CU.4: 5 residues within 4Å: Chain A: W.48, H.80, A.120, H.128, M.133 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.80, A:H.128 CU.5: 7 residues within 4Å: Chain A: D.83, H.85, H.119 Chain B: H.229, H.279, F.281 Ligands: NO2.3 7 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:H.85, A:H.119, B:H.279, H2O.1, H2O.1, H2O.10, H2O.10 CU.6: 3 residues within 4Å: Chain A: V.21, H.27, H.68 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.27, A:H.68, H2O.10, H2O.10 CU.10: 5 residues within 4Å: Chain B: W.48, H.80, A.120, H.128, M.133 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.80, B:H.128 CU.11: 7 residues within 4Å: Chain B: D.83, H.85, H.119 Chain C: H.229, H.279, F.281 Ligands: NO2.9 7 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: B:H.85, B:H.119, C:H.279, H2O.13, H2O.13, H2O.23, H2O.23 CU.12: 3 residues within 4Å: Chain B: V.21, H.27, H.68 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.27, B:H.68, H2O.22, H2O.22 CU.16: 5 residues within 4Å: Chain C: W.48, H.80, A.120, H.128, M.133 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.80, C:H.128 CU.17: 7 residues within 4Å: Chain A: H.229, H.279, F.281 Chain C: D.83, H.85, H.119 Ligands: NO2.15 7 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: C:H.85, C:H.119, A:H.279, H2O.26, H2O.26, H2O.36, H2O.36 CU.18: 3 residues within 4Å: Chain C: V.21, H.27, H.68 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.27, C:H.68, H2O.35, H2O.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom. J.Biol.Chem. (2025)

Release Date

2025-06-11

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Copper-containing nitrite reductase