SMTL ID : 5ytn.1

C135A mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans in complex with peroxide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: 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: 5 residues within 4Å: Chain A: H.100, H.134 Chain B: H.244, H.294 Ligands: PEO.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.294, A:H.100, A:H.134 CU.3: 2 residues within 4Å: Chain A: H.42, H.83 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.42, A:H.83 CU.6: 4 residues within 4Å: Chain B: 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: 5 residues within 4Å: Chain B: H.100, H.134 Chain C: H.244, H.294 Ligands: PEO.10 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.294, B:H.100, B:H.134 CU.8: 2 residues within 4Å: Chain B: H.42, H.83 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.42, B:H.83 CU.11: 4 residues within 4Å: Chain C: 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: 5 residues within 4Å: Chain A: H.244, H.294 Chain C: H.100, H.134 Ligands: PEO.15 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.100, C:H.134, A:H.294 CU.13: 2 residues within 4Å: Chain C: H.42, H.83 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.42, C:H.83

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

MRD.4: 6 residues within 4Å: Chain A: D.163, V.166, D.167, R.168, E.169, R.229 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.166 Hydrogen bonds: A:D.163, A:R.229 MRD.9: 6 residues within 4Å: Chain B: D.163, V.166, D.167, R.168, E.169, R.229 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.166 Hydrogen bonds: B:D.163, B:R.229 MRD.14: 6 residues within 4Å: Chain C: D.163, V.166, D.167, R.168, E.169, R.229 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.166 Hydrogen bonds: C:D.163, C:R.229

3 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.5: 9 residues within 4Å: Chain A: D.98, H.100, H.134 Chain B: H.244, V.246, V.292, H.294, F.296 Ligands: CU.2 No protein-ligand interaction detected (PLIP) PEO.10: 9 residues within 4Å: Chain B: D.98, H.100, H.134 Chain C: H.244, V.246, V.292, H.294, F.296 Ligands: CU.7 No protein-ligand interaction detected (PLIP) PEO.15: 9 residues within 4Å: Chain A: H.244, V.246, V.292, H.294, F.296 Chain C: D.98, H.100, H.134 Ligands: CU.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-08-22

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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