SMTL ID : 9kvm.1

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

Coordinates

PDB Format Compare

Method

NEUTRON DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

12 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: 7 residues within 4Å: Chain A: D.98, H.100, H.134 Chain B: H.244, H.294 Ligands: CU.4, FMT.5 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.294, A:H.100, A:H.134, H2O.1, H2O.8 CU.3: 2 residues within 4Å: Chain A: 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.4, H2O.8 CU.4: 7 residues within 4Å: Chain A: D.98, H.100 Chain B: H.244, V.245, V.246, G.247 Ligands: CU.2 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.244, H2O.1, H2O.4 CU.6: 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.7: 7 residues within 4Å: Chain B: D.98, H.100, H.134 Chain C: H.244, H.294 Ligands: CU.9, FMT.10 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.294, B:H.100, B:H.134, H2O.9, H2O.17 CU.8: 2 residues within 4Å: Chain B: 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.13, H2O.16 CU.9: 7 residues within 4Å: Chain B: D.98, H.100 Chain C: H.244, V.245, V.246, G.247 Ligands: CU.7 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.244, H2O.9, H2O.13 CU.11: 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.12: 7 residues within 4Å: Chain A: H.244, H.294 Chain C: D.98, H.100, H.134 Ligands: CU.14, FMT.15 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.100, C:H.134, A:H.294, H2O.18, H2O.25 CU.13: 2 residues within 4Å: Chain C: 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.22, H2O.25 CU.14: 7 residues within 4Å: Chain A: H.244, V.245, V.246, G.247 Chain C: D.98, H.100 Ligands: CU.12 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.244, H2O.18, H2O.21

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

FMT.5: 9 residues within 4Å: Chain A: D.98, H.134, V.140 Chain B: H.244, V.246, V.292, H.294, F.296 Ligands: CU.2 No protein-ligand interaction detected (PLIP) FMT.10: 9 residues within 4Å: Chain B: D.98, H.134, V.140 Chain C: H.244, V.246, V.292, H.294, F.296 Ligands: CU.7 No protein-ligand interaction detected (PLIP) FMT.15: 9 residues within 4Å: Chain A: H.244, V.246, V.292, H.294, F.296 Chain C: D.98, H.134, V.140 Ligands: CU.12 No protein-ligand interaction detected (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

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