SMTL ID : 6zua.1

Cu nitrite reductase from Achromobacter cycloclastes: MSOX series at 170K, dose point 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.14 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.89, C.130, H.139, M.144 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.89, A:C.130, A:H.139 CU.2: 6 residues within 4Å: Chain A: D.92, H.94, H.129 Chain B: H.300 Ligands: NO2.4, NO.7 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:H.94, A:H.129, B:H.300, NO.7, H2O.12 CU.8: 4 residues within 4Å: Chain B: H.89, C.130, H.139, M.144 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.89, B:C.130, B:H.139 CU.9: 6 residues within 4Å: Chain B: D.92, H.94, H.129 Chain C: H.300 Ligands: NO2.11, NO.14 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:H.300, B:H.94, B:H.129, NO.14, H2O.35 CU.15: 4 residues within 4Å: Chain C: H.89, C.130, H.139, M.144 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.89, C:C.130, C:H.139 CU.16: 6 residues within 4Å: Chain A: H.300 Chain C: D.92, H.94, H.129 Ligands: NO2.18, NO.21 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:H.94, C:H.129, A:H.300, NO.21, H2O.58

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: P.152, R.153, D.154 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.154 Water bridges: A:R.153, A:R.153, A:D.154, A:K.157, A:K.157, A:K.157 Salt bridges: A:K.157 SO4.5: 4 residues within 4Å: Chain A: D.182, E.183, K.188, K.202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.183 Water bridges: A:K.202 Salt bridges: A:K.188, A:K.202 SO4.10: 3 residues within 4Å: Chain B: P.152, R.153, D.154 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.154 Water bridges: B:R.153, B:R.153, B:D.154, B:D.154, B:K.157, B:K.157 Salt bridges: B:K.157 SO4.12: 4 residues within 4Å: Chain B: D.182, E.183, K.188, K.202 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.183 Water bridges: B:K.202 Salt bridges: B:K.188, B:K.202 SO4.17: 3 residues within 4Å: Chain C: P.152, R.153, D.154 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.154 Water bridges: C:R.153, C:R.153, C:D.154, C:D.154, C:K.157, C:K.157 Salt bridges: C:K.157 SO4.19: 4 residues within 4Å: Chain C: D.182, E.183, K.188, K.202 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.183 Water bridges: C:K.202 Salt bridges: C:K.188, C:K.202

3 x NO2: NITRITE ION(Non-covalent)

NO2.4: 9 residues within 4Å: Chain A: D.92, H.94, H.129 Chain B: H.249, I.251, H.300, L.302 Ligands: CU.2, NO.7 No protein-ligand interaction detected (PLIP) NO2.11: 9 residues within 4Å: Chain B: D.92, H.94, H.129 Chain C: H.249, I.251, H.300, L.302 Ligands: CU.9, NO.14 No protein-ligand interaction detected (PLIP) NO2.18: 9 residues within 4Å: Chain A: H.249, I.251, H.300, L.302 Chain C: D.92, H.94, H.129 Ligands: CU.16, NO.21 No protein-ligand interaction detected (PLIP)

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.6: 5 residues within 4Å: Chain A: G.219, T.222, F.306, A.311, H.313 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.311 Water bridges: A:G.219, A:G.309, A:A.311 Salt bridges: A:H.313, A:H.313 MLI.13: 5 residues within 4Å: Chain B: G.219, T.222, F.306, A.311, H.313 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.311 Water bridges: B:G.219, B:G.309, B:A.311 Salt bridges: B:H.313, B:H.313 MLI.20: 5 residues within 4Å: Chain C: G.219, T.222, F.306, A.311, H.313 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:A.311 Water bridges: C:G.219, C:G.309, C:A.311 Salt bridges: C:H.313, C:H.313

3 x NO: NITRIC OXIDE(Non-covalent)

NO.7: 8 residues within 4Å: Chain A: D.92, H.94, H.129 Chain B: H.249, I.251, H.300 Ligands: CU.2, NO2.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.92 NO.14: 8 residues within 4Å: Chain B: D.92, H.94, H.129 Chain C: H.249, I.251, H.300 Ligands: CU.9, NO2.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.92 NO.21: 8 residues within 4Å: Chain A: H.249, I.251, H.300 Chain C: D.92, H.94, H.129 Ligands: CU.16, NO2.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hough, M.A. et al., Nature of the copper-nitrosyl intermediates of copper nitrite reductases during catalysis. Chem Sci (2020)

Release Date

2021-06-23

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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