SMTL ID : 9kwu.1

D98N/C135A mutant of a copper-containing nitrite reductase in complex with nitrite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: W.63, H.95, A.135, H.143, M.148 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.95, A:H.143 CU.2: 8 residues within 4Å: Chain A: N.98, H.100, H.134 Chain C: H.244, H.294, F.296 Ligands: NO2.4, NO2.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.100, A:H.134, C:H.294 CU.6: 2 residues within 4Å: Chain A: P.38, H.39 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.39, H2O.3, H2O.10, H2O.11, H2O.13 CU.7: 3 residues within 4Å: Chain A: V.36, H.42, H.83 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.42, A:H.83, H2O.10 CU.8: 3 residues within 4Å: Chain A: D.167, E.226, K.227 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.167, H2O.1, H2O.7, H2O.11, H2O.13 CU.9: 5 residues within 4Å: Chain B: W.63, H.95, A.135, H.143, M.148 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.95, B:H.143 CU.10: 8 residues within 4Å: Chain A: H.244, H.294, F.296 Chain B: N.98, H.100, H.134 Ligands: NO2.12, NO2.13 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.100, B:H.134, A:H.294 CU.14: 2 residues within 4Å: Chain B: P.38, H.39 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.39, H2O.18, H2O.25, H2O.26, H2O.28 CU.15: 3 residues within 4Å: Chain B: V.36, H.42, H.83 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.42, B:H.83, H2O.26 CU.16: 3 residues within 4Å: Chain B: D.167, E.226, K.227 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.167, H2O.16, H2O.22, H2O.26, H2O.28 CU.17: 5 residues within 4Å: Chain C: W.63, H.95, A.135, H.143, M.148 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.95, C:H.143 CU.18: 8 residues within 4Å: Chain B: H.244, H.294, F.296 Chain C: N.98, H.100, H.134 Ligands: NO2.20, NO2.21 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.100, C:H.134, B:H.294 CU.22: 2 residues within 4Å: Chain C: P.38, H.39 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.39, H2O.33, H2O.40, H2O.41, H2O.43 CU.23: 3 residues within 4Å: Chain C: V.36, H.42, H.83 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.42, C:H.83, H2O.41 CU.24: 3 residues within 4Å: Chain C: D.167, E.226, K.227 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.167, H2O.32, H2O.37, H2O.41, H2O.44

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

MPD.3: 7 residues within 4Å: Chain A: D.163, V.166, D.167, R.168, E.169, R.229, Y.231 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.163, A:V.166 Hydrogen bonds: A:E.169 Water bridges: A:E.169, A:E.169 MPD.11: 7 residues within 4Å: Chain B: D.163, V.166, D.167, R.168, E.169, R.229, Y.231 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.163, B:V.166 Hydrogen bonds: B:E.169 Water bridges: B:E.169, B:E.169 MPD.19: 7 residues within 4Å: Chain C: D.163, V.166, D.167, R.168, E.169, R.229, Y.231 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:D.163, C:V.166 Hydrogen bonds: C:E.169 Water bridges: C:E.169, C:E.169

6 x NO2: NITRITE ION(Non-covalent)

NO2.4: 11 residues within 4Å: Chain A: N.98, H.100, H.134, V.140 Chain C: H.244, V.246, V.292, H.294, F.296 Ligands: CU.2, NO2.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.98 NO2.5: 9 residues within 4Å: Chain A: N.98, H.100, F.110, H.134 Chain C: H.244, V.246, G.247 Ligands: CU.2, NO2.4 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.98, C:H.244 NO2.12: 11 residues within 4Å: Chain A: H.244, V.246, V.292, H.294, F.296 Chain B: N.98, H.100, H.134, V.140 Ligands: CU.10, NO2.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.98 NO2.13: 9 residues within 4Å: Chain A: H.244, V.246, G.247 Chain B: N.98, H.100, F.110, H.134 Ligands: CU.10, NO2.12 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.98, A:H.244 NO2.20: 11 residues within 4Å: Chain B: H.244, V.246, V.292, H.294, F.296 Chain C: N.98, H.100, H.134, V.140 Ligands: CU.18, NO2.21 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.98 NO2.21: 9 residues within 4Å: Chain B: H.244, V.246, G.247 Chain C: N.98, H.100, F.110, H.134 Ligands: CU.18, NO2.20 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.98, B:H.244

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