SMTL ID : 9kwv.1

Structure of a D98N/C135A/G136A mutant copper-containing nitrite reductase in complex with nitrite

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.99 Å

Oligo State

homo-trimer

Ligands

18 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, CL.10 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.100, A:H.134, C:H.294, H2O.1 CU.6: 3 residues within 4Å: Chain A: V.36, H.42, H.83 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.42, A:H.83, H2O.7, H2O.11 CU.7: 2 residues within 4Å: Chain A: P.38, H.39 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.39, H2O.11, H2O.11 CU.8: 5 residues within 4Å: Chain A: T.248, V.249, F.281, T.282 Chain B: H.103 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:T.248, A:V.249, B:H.103, H2O.2 CU.9: 3 residues within 4Å: Chain A: D.167, E.226, K.227 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.167, H2O.1, H2O.7, H2O.11 CU.11: 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.12: 8 residues within 4Å: Chain A: H.244, H.294, F.296 Chain B: N.98, H.100, H.134 Ligands: NO2.14, CL.20 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.100, B:H.134, A:H.294, H2O.15 CU.16: 3 residues within 4Å: Chain B: V.36, H.42, H.83 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.42, B:H.83, H2O.21, H2O.25 CU.17: 2 residues within 4Å: Chain B: P.38, H.39 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.39, H2O.25, H2O.26 CU.18: 5 residues within 4Å: Chain B: T.248, V.249, F.281, T.282 Chain C: H.103 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.103, B:T.248, B:V.249, H2O.16 CU.19: 3 residues within 4Å: Chain B: D.167, E.226, K.227 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.167, H2O.15, H2O.22, H2O.25 CU.21: 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.22: 8 residues within 4Å: Chain B: H.244, H.294, F.296 Chain C: N.98, H.100, H.134 Ligands: NO2.24, CL.30 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.100, C:H.134, B:H.294, H2O.30 CU.26: 3 residues within 4Å: Chain C: V.36, H.42, H.83 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.42, C:H.83, H2O.35, H2O.40 CU.27: 2 residues within 4Å: Chain C: P.38, H.39 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.39, H2O.39, H2O.40 CU.28: 5 residues within 4Å: Chain A: H.103 Chain C: T.248, V.249, F.281, T.282 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.103, C:T.248, C:V.249, H2O.31 CU.29: 3 residues within 4Å: Chain C: D.167, E.226, K.227 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.167, H2O.29, H2O.36, H2O.40

6 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.5: 6 residues within 4Å: Chain A: D.251, T.282, T.284 Chain B: H.103, N.126, K.127 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.103, B:K.127 Water bridges: B:H.103, B:N.126 Hydrophobic interactions: A:T.284 MPD.13: 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.15: 6 residues within 4Å: Chain B: D.251, T.282, T.284 Chain C: H.103, N.126, K.127 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:H.103, C:K.127 Water bridges: C:H.103, C:N.126 Hydrophobic interactions: B:T.284 MPD.23: 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 MPD.25: 6 residues within 4Å: Chain A: H.103, N.126, K.127 Chain C: D.251, T.282, T.284 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:H.103, A:K.127 Water bridges: A:H.103, A:N.126 Hydrophobic interactions: C:T.284

3 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, CL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.98 NO2.14: 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.12, CL.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.98 NO2.24: 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.22, CL.30 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.98

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

CL.10: 10 residues within 4Å: Chain A: N.98, H.100, H.134 Chain C: H.244, V.246, V.292, H.294, F.296 Ligands: CU.2, NO2.4 Ligand excluded by PLIP CL.20: 10 residues within 4Å: Chain A: H.244, V.246, V.292, H.294, F.296 Chain B: N.98, H.100, H.134 Ligands: CU.12, NO2.14 Ligand excluded by PLIP CL.30: 10 residues within 4Å: Chain B: H.244, V.246, V.292, H.294, F.296 Chain C: N.98, H.100, H.134 Ligands: CU.22, NO2.24 Ligand excluded by PLIP

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